Mercurial > repos > iuc > enasearch_retrieve_run_report
view search_macros.xml @ 2:3dd81790a236 draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/enasearch commit a0adc28145cce02ecaed3a90156ed54c4385d1a0"
author | iuc |
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date | Tue, 21 Jan 2020 19:06:02 -0500 |
parents | c320e878909a |
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<?xml version="1.0" ?> <macros> <xml name="analysis_fields"> <option value="analysis_accession">analysis_accession</option> <option value="study_accession">study_accession</option> <option value="secondary_study_accession">secondary_study_accession</option> <option value="sample_accession">sample_accession</option> <option value="secondary_sample_accession">secondary_sample_accession</option> <option value="analysis_title">analysis_title</option> <option value="analysis_type">analysis_type</option> <option value="center_name">center_name</option> <option value="first_public">first_public</option> <option value="last_updated">last_updated</option> <option value="study_title">study_title</option> <option value="tax_id">tax_id</option> <option value="scientific_name">scientific_name</option> <option value="analysis_alias">analysis_alias</option> <option value="study_alias">study_alias</option> <option value="submitted_bytes">submitted_bytes</option> <option value="submitted_md5">submitted_md5</option> <option value="submitted_ftp">submitted_ftp</option> <option value="submitted_aspera">submitted_aspera</option> <option value="submitted_galaxy">submitted_galaxy</option> <option value="sample_alias">sample_alias</option> <option value="broker_name">broker_name</option> </xml> <xml name="display_options"> <option value="xml">Results are displayed in XML format. Supported by all ENA data classes.</option> <option value="text">Results are displayed in text format. Supported only by assembled and annotated sequence data classes.</option> <option value="fastq">Results are displayed in fastq format. Supported only by Trace data class.</option> <option value="html">Results are displayed in HTML format. Supported by all ENA data classes. HTML is the default display format if no other display option has been specified.</option> <option value="report">Results are displayed as a tab separated report</option> <option value="fasta">Results are displayed in fasta format. Supported by assembled and annotated sequence and Trace data classes.</option> </xml> <xml name="when_display_options"> <when value="xml"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> </when> <when value="text"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> </when> <when value="fastq"> <param name="range_start" argument="--subseq_range" type="integer" optional="true" label="Start integer for subsequences"/> <param name="range_stop" argument="--subseq_range" type="integer" optional="true" label="Stop integer for subsequences"/> </when> <when value="html"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> </when> <when value="report"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> </when> <when value="fasta"> <param name="range_start" argument="--subseq_range" type="integer" optional="true" label="Start integer for subsequences"/> <param name="range_stop" argument="--subseq_range" type="integer" optional="true" label="Stop integer for subsequences"/> </when> </xml> <xml name="run_fields"> <option value="study_accession">study_accession</option> <option value="secondary_study_accession">secondary_study_accession</option> <option value="sample_accession">sample_accession</option> <option value="secondary_sample_accession">secondary_sample_accession</option> <option value="experiment_accession">experiment_accession</option> <option value="run_accession">run_accession</option> <option value="submission_accession">submission_accession</option> <option value="tax_id">tax_id</option> <option value="scientific_name">scientific_name</option> <option value="instrument_platform">instrument_platform</option> <option value="instrument_model">instrument_model</option> <option value="library_name">library_name</option> <option value="nominal_length">nominal_length</option> <option value="library_layout">library_layout</option> <option value="library_strategy">library_strategy</option> <option value="library_source">library_source</option> <option value="library_selection">library_selection</option> <option value="read_count">read_count</option> <option value="base_count">base_count</option> <option value="center_name">center_name</option> <option value="first_public">first_public</option> <option value="last_updated">last_updated</option> <option value="experiment_title">experiment_title</option> <option value="study_title">study_title</option> <option value="study_alias">study_alias</option> <option value="experiment_alias">experiment_alias</option> <option value="run_alias">run_alias</option> <option value="fastq_bytes">fastq_bytes</option> <option value="fastq_md5">fastq_md5</option> <option value="fastq_ftp">fastq_ftp</option> <option value="fastq_aspera">fastq_aspera</option> <option value="fastq_galaxy">fastq_galaxy</option> <option value="submitted_bytes">submitted_bytes</option> <option value="submitted_md5">submitted_md5</option> <option value="submitted_ftp">submitted_ftp</option> <option value="submitted_aspera">submitted_aspera</option> <option value="submitted_galaxy">submitted_galaxy</option> <option value="submitted_format">submitted_format</option> <option value="sra_bytes">sra_bytes</option> <option value="sra_md5">sra_md5</option> <option value="sra_ftp">sra_ftp</option> <option value="sra_aspera">sra_aspera</option> <option value="sra_galaxy">sra_galaxy</option> <option value="cram_index_ftp">cram_index_ftp</option> <option value="cram_index_aspera">cram_index_aspera</option> <option value="cram_index_galaxy">cram_index_galaxy</option> <option value="sample_alias">sample_alias</option> <option value="broker_name">broker_name</option> </xml> <xml name="taxonomy_results"> <option value="noncoding_release">Non-coding sequences (Release)</option> <option value="sequence_release">Nucleotide Sequences (Release)</option> <option value="study">Studies</option> <option value="read_trace">Capillary Traces in Trace Archive</option> <option value="coding_release">Protein-coding sequences (Release)</option> <option value="sample">Samples</option> <option value="read_run">Raw reads</option> <option value="read_study">Raw reads (grouped by study)</option> <option value="read_experiment">Raw reads (grouped by experiment)</option> <option value="analysis">Nucleotide sequence analyses</option> <option value="sequence_update">Nucleotide Sequences (Update)</option> <option value="coding_update">Protein-coding sequences (Update)</option> <option value="analysis_study">Nucleotide sequence analyses (grouped by study)</option> <option value="noncoding_update">Non-coding sequences (Update)</option> </xml> <xml name="free_text_search"> <conditional name="res"> <param argument="--result" type="select" label="Result to return"> <option value="noncoding_release">Non-coding sequences (Release)</option> <option value="assembly">Genome assemblies</option> <option value="sequence_release">Nucleotide sequences (Release)</option> <option value="wgs_set">Genome assembly contig set</option> <option value="study">Studies</option> <option value="taxon">Taxonomic classification</option> <option value="coding_release">Protein-coding sequences (Release)</option> <option value="sample">Samples</option> <option value="environmental">Environmental samples</option> <option value="read_run">Raw reads</option> <option value="read_study">Raw reads (grouped by study)</option> <option value="read_experiment">Raw reads (grouped by experiment)</option> <option value="analysis">Nucleotide sequence analyses from reads</option> <option value="sequence_update">Nucleotide sequences (Update)</option> <option value="coding_update">Protein-coding sequences (Update)</option> <option value="tsa_set">Transcriptome assembly contig set</option> <option value="analysis_study">Nucleotide sequence analyses from reads (grouped by study)</option> <option value="noncoding_update">Non-coding sequences (Update)</option> </param> <when value="noncoding_release"> <conditional name="display_opt"> <param argument="--display" type="select" label="Display option to specify the display format"> <expand macro="display_options"/> </param> <when value="xml"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> </when> <when value="text"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> </when> <when value="fastq"/> <when value="html"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> </when> <when value="report"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> <param argument="--fields" type="select" multiple="true" label="Fields to return"> <option value="accession">accession</option> <option value="base_count">base_count</option> <option value="collected_by">collected_by</option> <option value="dataclass">dataclass</option> <option value="first_public">first_public</option> <option value="last_updated">last_updated</option> <option value="location">location</option> <option value="tax_division">tax_division</option> <option value="tax_id">tax_id</option> <option value="scientific_name">scientific_name</option> <option value="rna_class">rna_class</option> <option value="gene">gene</option> <option value="gene_synonym">gene_synonym</option> <option value="product">product</option> <option value="anticodon">anticodon</option> <option value="function">function</option> <option value="locus_tag">locus_tag</option> <option value="experiment">experiment</option> <option value="inference">inference</option> <option value="note">note</option> <option value="bio_material">bio_material</option> <option value="cell_line">cell_line</option> <option value="cell_type">cell_type</option> <option value="country">country</option> <option value="cultivar">cultivar</option> <option value="culture_collection">culture_collection</option> <option value="description">description</option> <option value="dev_stage">dev_stage</option> <option value="ecotype">ecotype</option> <option value="environmental_sample">environmental_sample</option> <option value="germline">germline</option> <option value="host">host</option> <option value="identified_by">identified_by</option> <option value="isolate">isolate</option> <option value="isolation_source">isolation_source</option> <option value="keywords">keywords</option> <option value="lab_host">lab_host</option> <option value="mating_type">mating_type</option> <option value="mol_type">mol_type</option> <option value="organelle">organelle</option> <option value="serotype">serotype</option> <option value="serovar">serovar</option> <option value="sex">sex</option> <option value="collection_date">collection_date</option> <option value="submitted_sex">submitted_sex</option> <option value="specimen_voucher">specimen_voucher</option> <option value="strain">strain</option> <option value="sub_species">sub_species</option> <option value="sub_strain">sub_strain</option> <option value="tissue_lib">tissue_lib</option> <option value="tissue_type">tissue_type</option> <option value="topology">topology</option> <option value="variety">variety</option> <option value="sequence_md5">sequence_md5</option> <option value="study_accession">study_accession</option> </param> <param argument="--sortfields" type="select" optional="true" multiple="true" label="Fields to sort the results"> <option value="mol_type">in vivo molecule type of the sequence</option> <option value="last_updated">date when last updated</option> <option value="sequence_md5"></option> <option value="collected_by">name of the person who collected the specimen</option> <option value="serotype">serological variety of a species characterized by its antigenic properties</option> <option value="sex">sex of the organism from which the sample was obtained</option> <option value="keywords">keywords associated with sequence</option> <option value="cell_line">cell line from which the sample was obtained</option> <option value="inference">a structured description of non-experimental evidence</option> <option value="bio_material">identifier for biological material including institute and collection code</option> <option value="identified_by">name of the taxonomist who identified the specimen</option> <option value="note">any comment or additional information</option> <option value="locus_tag">a submitter-supplied, systematic, stable identifier for a gene and its associated features</option> <option value="lab_host">scientific name of the laboratory host used to propagate the source organism for the sample</option> <option value="tax_division">taxonomic division</option> <option value="collection_date">date that the specimen was collected</option> <option value="specimen_voucher">identifier for the sample culture including institute and collection code</option> <option value="dev_stage">sample obtained from an organism in a specific developmental stage</option> <option value="isolate">individual isolate from which sample was obtained</option> <option value="anticodon">location of the anticodon of tRNA and the amino acid for which it codes</option> <option value="experiment">a brief description of the nature of the experimental evidence</option> <option value="location">geographic location of isolation of the sample</option> <option value="study_accession">study accession number</option> <option value="function">function attributed to a sequence</option> <option value="germline">the sample is an unrearranged molecule that was inherited from the parental germline</option> <option value="product">name of the product associated with the feature</option> <option value="description">brief sequence description</option> <option value="ecotype">a population within a given species displaying traits that reflect adaptation to a local habitat</option> <option value="cell_type">cell type from which the sample was obtained</option> <option value="accession">accession number</option> <option value="isolation_source">describes the physical, environmental and/or local geographical source of the sample</option> <option value="mating_type">mating type of the organism from which the sequence was obtained</option> <option value="tissue_type">tissue type from which the sample was obtained</option> <option value="sub_strain">name or identifier of a genetically or otherwise modified strain from which sample was obtained</option> <option value="tissue_lib">tissue library from which sample was obtained</option> <option value="cultivar">cultivar (cultivated variety) of plant from which sample was obtained</option> <option value="base_count">number of base pairs</option> <option value="topology">sequence topology: circular or linear</option> <option value="sub_species">name of sub-species of organism from which sample was obtained</option> <option value="environmental_sample">identifies sequences derived by direct molecular isolation from an environmental DNA sample</option> <option value="first_public">date when made public</option> <option value="strain">strain from which sample was obtained</option> <option value="country">locality of sample isolation: country names, oceans or seas, followed by regions and localities</option> <option value="variety">variety (varietas, a formal Linnaean rank) of organism from which sample was derived</option> <option value="host">natural (as opposed to laboratory) host to the organism from which sample was obtained</option> <option value="gene_synonym">synonymous, replaced, obsolete or former gene symbol</option> <option value="organelle">membrane-bound intracellular structure from which the sequence was obtained</option> <option value="serovar">serological variety of a species (usually a prokaryote) characterized by its antigenic properties</option> <option value="rna_class">classification of RNA</option> <option value="dataclass">sequence data class</option> <option value="gene">symbol of the gene corresponding to a sequence region</option> <option value="culture_collection">identifier for the sample culture including institute and collection code</option> </param> </when> <when value="fasta"/> </conditional> </when> <when value="assembly"> <conditional name="display_opt"> <param argument="--display" type="select" label="Display option to specify the display format"> <expand macro="display_options"/> </param> <when value="xml"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> </when> <when value="text"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> </when> <when value="fastq"/> <when value="html"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> </when> <when value="report"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> <param argument="--fields" type="select" multiple="true" label="Fields to return"> <option value="accession">accession</option> <option value="study_accession">study_accession</option> <option value="sample_accession">sample_accession</option> <option value="assembly_name">assembly_name</option> <option value="assembly_title">assembly_title</option> <option value="study_name">study_name</option> <option value="study_title">study_title</option> <option value="study_description">study_description</option> <option value="tax_id">tax_id</option> <option value="scientific_name">scientific_name</option> <option value="strain">strain</option> <option value="base_count">base_count</option> <option value="assembly_level">assembly_level</option> <option value="genome_representation">genome_representation</option> </param> <param argument="--sortfields" type="select" optional="true" multiple="true" label="Fields to sort the results"> <option value="assembly_name">genome assembly name for all live versions</option> <option value="base_count">number of base pairs</option> <option value="strain">strain from which sample was obtained</option> <option value="study_description">detailed sequencing study description</option> <option value="accession">accession number</option> <option value="assembly_level">assembly level</option> <option value="sample_accession">sample accession number</option> <option value="assembly_title">brief genome assembly description</option> <option value="study_title">brief sequencing study description</option> <option value="genome_representation">whether this is a full or partial genome</option> <option value="study_name">sequencing study name</option> <option value="study_accession">study accession number</option> </param> </when> <when value="fasta"/> </conditional> </when> <when value="sequence_release"> <conditional name="display_opt"> <param argument="--display" type="select" label="Display option to specify the display format"> <expand macro="display_options"/> </param> <when value="xml"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> </when> <when value="text"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> </when> <when value="fastq"/> <when value="html"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> </when> <when value="report"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> <param argument="--fields" type="select" multiple="true" label="Fields to return"> <option value="accession">accession</option> <option value="base_count">base_count</option> <option value="bio_material">bio_material</option> <option value="cell_line">cell_line</option> <option value="cell_type">cell_type</option> <option value="collected_by">collected_by</option> <option value="collection_date">collection_date</option> <option value="country">country</option> <option value="cultivar">cultivar</option> <option value="culture_collection">culture_collection</option> <option value="dataclass">dataclass</option> <option value="description">description</option> <option value="dev_stage">dev_stage</option> <option value="ecotype">ecotype</option> <option value="environmental_sample">environmental_sample</option> <option value="first_public">first_public</option> <option value="germline">germline</option> <option value="host">host</option> <option value="identified_by">identified_by</option> <option value="isolate">isolate</option> <option value="isolation_source">isolation_source</option> <option value="keywords">keywords</option> <option value="lab_host">lab_host</option> <option value="last_updated">last_updated</option> <option value="location">location</option> <option value="mating_type">mating_type</option> <option value="mol_type">mol_type</option> <option value="organelle">organelle</option> <option value="serotype">serotype</option> <option value="serovar">serovar</option> <option value="sex">sex</option> <option value="submitted_sex">submitted_sex</option> <option value="specimen_voucher">specimen_voucher</option> <option value="strain">strain</option> <option value="sub_species">sub_species</option> <option value="sub_strain">sub_strain</option> <option value="tax_division">tax_division</option> <option value="tissue_lib">tissue_lib</option> <option value="tissue_type">tissue_type</option> <option value="topology">topology</option> <option value="variety">variety</option> <option value="tax_id">tax_id</option> <option value="scientific_name">scientific_name</option> <option value="altitude">altitude</option> <option value="haplotype">haplotype</option> <option value="plasmid">plasmid</option> <option value="study_accession">study_accession</option> <option value="sequence_md5">sequence_md5</option> </param> <param argument="--sortfields" type="select" optional="true" multiple="true" label="Fields to sort the results"> <option value="mol_type">in vivo molecule type of the sequence</option> <option value="last_updated">date when last updated</option> <option value="sequence_md5"></option> <option value="haplotype">combination of alleles that are linked together on the same physical chromosome</option> <option value="serotype">serological variety of a species characterized by its antigenic properties</option> <option value="sex">sex of the organism from which the sample was obtained</option> <option value="keywords">keywords associated with sequence</option> <option value="collected_by">name of the person who collected the specimen</option> <option value="cell_line">cell line from which the sample was obtained</option> <option value="ecotype">a population within a given species displaying traits that reflect adaptation to a local habitat</option> <option value="bio_material">identifier for biological material including institute and collection code</option> <option value="identified_by">name of the taxonomist who identified the specimen</option> <option value="cell_type">cell type from which the sample was obtained</option> <option value="lab_host">scientific name of the laboratory host used to propagate the source organism for the sample</option> <option value="tax_division">taxonomic division</option> <option value="collection_date">date that the specimen was collected</option> <option value="specimen_voucher">identifier for the sample culture including institute and collection code</option> <option value="altitude">Altitude (m)</option> <option value="dev_stage">sample obtained from an organism in a specific developmental stage</option> <option value="isolate">individual isolate from which sample was obtained</option> <option value="location">geographic location of isolation of the sample</option> <option value="study_accession">study accession number</option> <option value="germline">the sample is an unrearranged molecule that was inherited from the parental germline</option> <option value="description">brief sequence description</option> <option value="accession">accession number</option> <option value="isolation_source">describes the physical, environmental and/or local geographical source of the sample</option> <option value="mating_type">mating type of the organism from which the sequence was obtained</option> <option value="tissue_type">tissue type from which the sample was obtained</option> <option value="sub_strain">name or identifier of a genetically or otherwise modified strain from which sample was obtained</option> <option value="tissue_lib">tissue library from which sample was obtained</option> <option value="cultivar">cultivar (cultivated variety) of plant from which sample was obtained</option> <option value="base_count">number of base pairs</option> <option value="topology">sequence topology: circular or linear</option> <option value="sub_species">name of sub-species of organism from which sample was obtained</option> <option value="environmental_sample">identifies sequences derived by direct molecular isolation from an environmental DNA sample</option> <option value="first_public">date when made public</option> <option value="strain">strain from which sample was obtained</option> <option value="country">locality of sample isolation: country names, oceans or seas, followed by regions and localities</option> <option value="variety">variety (varietas, a formal Linnaean rank) of organism from which sample was derived</option> <option value="host">natural (as opposed to laboratory) host to the organism from which sample was obtained</option> <option value="organelle">membrane-bound intracellular structure from which the sequence was obtained</option> <option value="serovar">serological variety of a species (usually a prokaryote) characterized by its antigenic properties</option> <option value="plasmid">name of naturally occurring plasmid from which the sequence was obtained</option> <option value="dataclass">sequence data class</option> <option value="culture_collection">identifier for the sample culture including institute and collection code</option> </param> </when> <when value="fasta"/> </conditional> </when> <when value="wgs_set"> <conditional name="display_opt"> <param argument="--display" type="select" label="Display option to specify the display format"> <expand macro="display_options"/> </param> <when value="xml"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> </when> <when value="text"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> </when> <when value="fastq"/> <when value="html"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> </when> <when value="report"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> <param argument="--fields" type="select" multiple="true" label="Fields to return"> <option value="accession">accession</option> <option value="bio_material">bio_material</option> <option value="cell_line">cell_line</option> <option value="cell_type">cell_type</option> <option value="collected_by">collected_by</option> <option value="collection_date">collection_date</option> <option value="country">country</option> <option value="cultivar">cultivar</option> <option value="culture_collection">culture_collection</option> <option value="description">description</option> <option value="dev_stage">dev_stage</option> <option value="ecotype">ecotype</option> <option value="environmental_sample">environmental_sample</option> <option value="first_public">first_public</option> <option value="germline">germline</option> <option value="host">host</option> <option value="identified_by">identified_by</option> <option value="isolate">isolate</option> <option value="isolation_source">isolation_source</option> <option value="keywords">keywords</option> <option value="lab_host">lab_host</option> <option value="last_updated">last_updated</option> <option value="location">location</option> <option value="mating_type">mating_type</option> <option value="mol_type">mol_type</option> <option value="serotype">serotype</option> <option value="serovar">serovar</option> <option value="sex">sex</option> <option value="submitted_sex">submitted_sex</option> <option value="specimen_voucher">specimen_voucher</option> <option value="strain">strain</option> <option value="sub_species">sub_species</option> <option value="sub_strain">sub_strain</option> <option value="tax_division">tax_division</option> <option value="tissue_lib">tissue_lib</option> <option value="tissue_type">tissue_type</option> <option value="variety">variety</option> <option value="tax_id">tax_id</option> <option value="scientific_name">scientific_name</option> <option value="altitude">altitude</option> <option value="haplotype">haplotype</option> <option value="study_accession">study_accession</option> <option value="set_files">set_files</option> </param> <param argument="--sortfields" type="select" optional="true" multiple="true" label="Fields to sort the results"> <option value="mol_type">in vivo molecule type of the sequence</option> <option value="last_updated">date when last updated</option> <option value="lab_host">scientific name of the laboratory host used to propagate the source organism for the sample</option> <option value="haplotype">combination of alleles that are linked together on the same physical chromosome</option> <option value="accession">accession number</option> <option value="sex">sex of the organism from which the sample was obtained</option> <option value="cell_line">cell line from which the sample was obtained</option> <option value="host">natural (as opposed to laboratory) host to the organism from which sample was obtained</option> <option value="ecotype">a population within a given species displaying traits that reflect adaptation to a local habitat</option> <option value="bio_material">identifier for biological material including institute and collection code</option> <option value="identified_by">name of the taxonomist who identified the specimen</option> <option value="cell_type">cell type from which the sample was obtained</option> <option value="tax_division">taxonomic division</option> <option value="collection_date">date that the specimen was collected</option> <option value="specimen_voucher">identifier for the sample culture including institute and collection code</option> <option value="altitude">Altitude (m)</option> <option value="dev_stage">sample obtained from an organism in a specific developmental stage</option> <option value="isolate">individual isolate from which sample was obtained</option> <option value="location">geographic location of isolation of the sample</option> <option value="study_accession">study accession number</option> <option value="germline">the sample is an unrearranged molecule that was inherited from the parental germline</option> <option value="description">brief sequence description</option> <option value="tissue_lib">tissue library from which sample was obtained</option> <option value="isolation_source">describes the physical, environmental and/or local geographical source of the sample</option> <option value="mating_type">mating type of the organism from which the sequence was obtained</option> <option value="serovar">serological variety of a species (usually a prokaryote) characterized by its antigenic properties</option> <option value="serotype">serological variety of a species characterized by its antigenic properties</option> <option value="sub_strain">name or identifier of a genetically or otherwise modified strain from which sample was obtained</option> <option value="cultivar">cultivar (cultivated variety) of plant from which sample was obtained</option> <option value="collected_by">name of the person who collected the specimen</option> <option value="sub_species">name of sub-species of organism from which sample was obtained</option> <option value="first_public">date when made public</option> <option value="strain">strain from which sample was obtained</option> <option value="country">locality of sample isolation: country names, oceans or seas, followed by regions and localities</option> <option value="variety">variety (varietas, a formal Linnaean rank) of organism from which sample was derived</option> <option value="environmental_sample">identifies sequences derived by direct molecular isolation from an environmental DNA sample</option> <option value="tissue_type">tissue type from which the sample was obtained</option> <option value="keywords">keywords associated with sequence</option> <option value="culture_collection">identifier for the sample culture including institute and collection code</option> </param> </when> <when value="fasta"/> </conditional> </when> <when value="study"> <conditional name="display_opt"> <param argument="--display" type="select" label="Display option to specify the display format"> <expand macro="display_options"/> </param> <when value="xml"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> </when> <when value="text"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> </when> <when value="fastq"/> <when value="html"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> </when> <when value="report"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> <param argument="--fields" type="select" multiple="true" label="Fields to return"> <option value="study_accession">study_accession</option> <option value="secondary_study_accession">secondary_study_accession</option> <option value="study_description">study_description</option> <option value="study_name">study_name</option> <option value="study_title">study_title</option> <option value="tax_id">tax_id</option> <option value="scientific_name">scientific_name</option> <option value="strain">strain</option> <option value="breed">breed</option> <option value="cultivar">cultivar</option> <option value="isolate">isolate</option> <option value="center_name">center_name</option> <option value="broker_name">broker_name</option> <option value="keywords">keywords</option> <option value="geo_accession">geo_accession</option> <option value="last_updated">last_updated</option> </param> <param argument="--sortfields" type="select" optional="true" multiple="true" label="Fields to sort the results"> <option value="broker_name">broker name</option> <option value="last_updated">date when last updated</option> <option value="center_name">Submitting center</option> <option value="study_description">detailed sequencing study description</option> <option value="breed">breed</option> <option value="isolate">individual isolate from which sample was obtained</option> <option value="study_name">sequencing study name</option> <option value="geo_accession">GEO accession</option> <option value="strain">strain from which sample was obtained</option> <option value="secondary_study_accession">project accession number</option> <option value="keywords">keywords associated with sequence</option> <option value="study_title">brief sequencing study description</option> <option value="cultivar">cultivar (cultivated variety) of plant from which sample was obtained</option> <option value="study_accession">study accession number</option> </param> </when> <when value="fasta"/> </conditional> </when> <when value="taxon"> <conditional name="display_opt"> <param argument="--display" type="select" label="Display option to specify the display format"> <expand macro="display_options"/> </param> <when value="xml"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> </when> <when value="text"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> </when> <when value="fastq"/> <when value="html"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> </when> <when value="report"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> <param argument="--fields" type="select" multiple="true" label="Fields to return"> <option value="tax_id">tax_id</option> <option value="taxon_title">taxon_title</option> <option value="scientific_name">scientific_name</option> </param> <param argument="--sortfields" type="select" optional="true" multiple="true" label="Fields to sort the results"> </param> </when> <when value="fasta"/> </conditional> </when> <when value="coding_release"> <conditional name="display_opt"> <param argument="--display" type="select" label="Display option to specify the display format"> <expand macro="display_options"/> </param> <when value="xml"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> </when> <when value="text"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> </when> <when value="fastq"/> <when value="html"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> </when> <when value="report"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> <param argument="--fields" type="select" multiple="true" label="Fields to return"> <option value="accession">accession</option> <option value="base_count">base_count</option> <option value="bio_material">bio_material</option> <option value="cell_line">cell_line</option> <option value="cell_type">cell_type</option> <option value="collected_by">collected_by</option> <option value="collection_date">collection_date</option> <option value="country">country</option> <option value="cultivar">cultivar</option> <option value="culture_collection">culture_collection</option> <option value="dataclass">dataclass</option> <option value="description">description</option> <option value="dev_stage">dev_stage</option> <option value="ecotype">ecotype</option> <option value="environmental_sample">environmental_sample</option> <option value="first_public">first_public</option> <option value="germline">germline</option> <option value="host">host</option> <option value="identified_by">identified_by</option> <option value="isolate">isolate</option> <option value="isolation_source">isolation_source</option> <option value="keywords">keywords</option> <option value="lab_host">lab_host</option> <option value="last_updated">last_updated</option> <option value="location">location</option> <option value="mating_type">mating_type</option> <option value="mol_type">mol_type</option> <option value="organelle">organelle</option> <option value="serotype">serotype</option> <option value="serovar">serovar</option> <option value="sex">sex</option> <option value="submitted_sex">submitted_sex</option> <option value="specimen_voucher">specimen_voucher</option> <option value="strain">strain</option> <option value="sub_species">sub_species</option> <option value="sub_strain">sub_strain</option> <option value="tax_division">tax_division</option> <option value="tissue_lib">tissue_lib</option> <option value="tissue_type">tissue_type</option> <option value="variety">variety</option> <option value="allele">allele</option> <option value="artificial_location">artificial_location</option> <option value="codon_start">codon_start</option> <option value="ec_number">ec_number</option> <option value="exception">exception</option> <option value="experiment">experiment</option> <option value="function">function</option> <option value="topology">topology</option> <option value="gene">gene</option> <option value="gene_synonym">gene_synonym</option> <option value="inference">inference</option> <option value="locus_tag">locus_tag</option> <option value="map">map</option> <option value="note">note</option> <option value="old_locus_tag">old_locus_tag</option> <option value="operon">operon</option> <option value="partial">partial</option> <option value="product">product</option> <option value="protein_id">protein_id</option> <option value="pseudo">pseudo</option> <option value="pseudo_gene">pseudo_gene</option> <option value="ribosomal_slippage">ribosomal_slippage</option> <option value="standard_name">standard_name</option> <option value="trans_splicing">trans_splicing</option> <option value="transl_except">transl_except</option> <option value="transl_table">transl_table</option> <option value="tax_id">tax_id</option> <option value="scientific_name">scientific_name</option> <option value="parent_accession">parent_accession</option> <option value="altitude">altitude</option> <option value="haplotype">haplotype</option> <option value="sequence_md5">sequence_md5</option> </param> <param argument="--sortfields" type="select" optional="true" multiple="true" label="Fields to sort the results"> <option value="operon">name of the group of contiguous genes transcribed into a single transcript</option> <option value="mol_type">in vivo molecule type of the sequence</option> <option value="last_updated">date when last updated</option> <option value="lab_host">scientific name of the laboratory host used to propagate the source organism for the sample</option> <option value="transl_except">a single codon translation that does not conform to genetic code</option> <option value="haplotype">combination of alleles that are linked together on the same physical chromosome</option> <option value="serotype">serological variety of a species characterized by its antigenic properties</option> <option value="trans_splicing">indicates exons from two RNA molecules are ligated in intermolecular reaction to form mature RNA</option> <option value="sex">sex of the organism from which the sample was obtained</option> <option value="pseudo_gene">indicates that this feature is a pseudogene</option> <option value="standard_name">accepted standard name for a feature</option> <option value="collected_by">name of the person who collected the specimen</option> <option value="germline">the sample is an unrearranged molecule that was inherited from the parental germline</option> <option value="cell_type">cell type from which the sample was obtained</option> <option value="host">natural (as opposed to laboratory) host to the organism from which sample was obtained</option> <option value="inference">a structured description of non-experimental evidence</option> <option value="bio_material">identifier for biological material including institute and collection code</option> <option value="parent_accession">parent sequence accession number</option> <option value="identified_by">name of the taxonomist who identified the specimen</option> <option value="locus_tag">a submitter-supplied, systematic, stable identifier for a gene and its associated features</option> <option value="sequence_md5"></option> <option value="tax_division">taxonomic division</option> <option value="old_locus_tag">deprecated submitter-supplied, systematic, stable identifier for a gene and its associated features</option> <option value="specimen_voucher">identifier for the sample culture including institute and collection code</option> <option value="altitude">Altitude (m)</option> <option value="dev_stage">sample obtained from an organism in a specific developmental stage</option> <option value="isolate">individual isolate from which sample was obtained</option> <option value="ec_number">Enzyme Commission number for enzyme product of sequence</option> <option value="note">any comment or additional information</option> <option value="experiment">a brief description of the nature of the experimental evidence</option> <option value="location">geographic location of isolation of the sample</option> <option value="collection_date">date that the specimen was collected</option> <option value="allele">name of the allele for the given gene</option> <option value="protein_id">a stable protein identifier issued by INSDC</option> <option value="partial">differentiates between complete regions and partial ones (deprecated qualifier)</option> <option value="artificial_location">indicates location is modified to adjust for the presence of a frameshift or internal stop codon</option> <option value="function">function attributed to a sequence</option> <option value="map">genomic map position of feature</option> <option value="product">name of the product associated with the feature</option> <option value="description">brief sequence description</option> <option value="cell_line">cell line from which the sample was obtained</option> <option value="gene_synonym">synonymous, replaced, obsolete or former gene symbol</option> <option value="ecotype">a population within a given species displaying traits that reflect adaptation to a local habitat</option> <option value="exception">indicates that the coding region cannot be translated using standard biological rules</option> <option value="accession">accession number</option> <option value="isolation_source">describes the physical, environmental and/or local geographical source of the sample</option> <option value="mating_type">mating type of the organism from which the sequence was obtained</option> <option value="tissue_type">tissue type from which the sample was obtained</option> <option value="sub_strain">name or identifier of a genetically or otherwise modified strain from which sample was obtained</option> <option value="tissue_lib">tissue library from which sample was obtained</option> <option value="cultivar">cultivar (cultivated variety) of plant from which sample was obtained</option> <option value="base_count">number of base pairs</option> <option value="topology">sequence topology: circular or linear</option> <option value="sub_species">name of sub-species of organism from which sample was obtained</option> <option value="first_public">date when made public</option> <option value="strain">strain from which sample was obtained</option> <option value="country">locality of sample isolation: country names, oceans or seas, followed by regions and localities</option> <option value="variety">variety (varietas, a formal Linnaean rank) of organism from which sample was derived</option> <option value="pseudo">the feature is non-functional</option> <option value="environmental_sample">identifies sequences derived by direct molecular isolation from an environmental DNA sample</option> <option value="transl_table">indicates the genetic code table used if other than universal genetic code table</option> <option value="organelle">membrane-bound intracellular structure from which the sequence was obtained</option> <option value="ribosomal_slippage">indicates ribosomal slippage (change to an alternative reading frame) during protein translation</option> <option value="serovar">serological variety of a species (usually a prokaryote) characterized by its antigenic properties</option> <option value="keywords">keywords associated with sequence</option> <option value="dataclass">sequence data class</option> <option value="gene">symbol of the gene corresponding to a sequence region</option> <option value="codon_start">indicates the offset of the first complete codon relative to the first base of the coding feature</option> <option value="culture_collection">identifier for the sample culture including institute and collection code</option> </param> </when> <when value="fasta"/> </conditional> </when> <when value="sample"> <conditional name="display_opt"> <param argument="--display" type="select" label="Display option to specify the display format"> <expand macro="display_options"/> </param> <when value="xml"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> </when> <when value="text"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> </when> <when value="fastq"/> <when value="html"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> </when> <when value="report"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> <param argument="--fields" type="select" multiple="true" label="Fields to return"> <option value="accession">accession</option> <option value="secondary_sample_accession">secondary_sample_accession</option> <option value="bio_material">bio_material</option> <option value="cell_line">cell_line</option> <option value="cell_type">cell_type</option> <option value="collected_by">collected_by</option> <option value="collection_date">collection_date</option> <option value="country">country</option> <option value="cultivar">cultivar</option> <option value="culture_collection">culture_collection</option> <option value="description">description</option> <option value="dev_stage">dev_stage</option> <option value="ecotype">ecotype</option> <option value="environmental_sample">environmental_sample</option> <option value="first_public">first_public</option> <option value="germline">germline</option> <option value="identified_by">identified_by</option> <option value="isolate">isolate</option> <option value="isolation_source">isolation_source</option> <option value="location">location</option> <option value="mating_type">mating_type</option> <option value="serotype">serotype</option> <option value="serovar">serovar</option> <option value="sex">sex</option> <option value="submitted_sex">submitted_sex</option> <option value="specimen_voucher">specimen_voucher</option> <option value="strain">strain</option> <option value="sub_species">sub_species</option> <option value="sub_strain">sub_strain</option> <option value="tissue_lib">tissue_lib</option> <option value="tissue_type">tissue_type</option> <option value="variety">variety</option> <option value="tax_id">tax_id</option> <option value="scientific_name">scientific_name</option> <option value="sample_alias">sample_alias</option> <option value="checklist">checklist</option> <option value="center_name">center_name</option> <option value="depth">depth</option> <option value="elevation">elevation</option> <option value="altitude">altitude</option> <option value="environment_biome">environment_biome</option> <option value="environment_feature">environment_feature</option> <option value="environment_material">environment_material</option> <option value="temperature">temperature</option> <option value="salinity">salinity</option> <option value="sampling_campaign">sampling_campaign</option> <option value="sampling_site">sampling_site</option> <option value="sampling_platform">sampling_platform</option> <option value="protocol_label">protocol_label</option> <option value="project_name">project_name</option> <option value="host">host</option> <option value="host_tax_id">host_tax_id</option> <option value="host_status">host_status</option> <option value="host_sex">host_sex</option> <option value="submitted_host_sex">submitted_host_sex</option> <option value="host_body_site">host_body_site</option> <option value="host_gravidity">host_gravidity</option> <option value="host_phenotype">host_phenotype</option> <option value="host_genotype">host_genotype</option> <option value="host_growth_conditions">host_growth_conditions</option> <option value="environmental_package">environmental_package</option> <option value="investigation_type">investigation_type</option> <option value="experimental_factor">experimental_factor</option> <option value="sample_collection">sample_collection</option> <option value="sequencing_method">sequencing_method</option> <option value="target_gene">target_gene</option> <option value="ph">ph</option> <option value="broker_name">broker_name</option> </param> <param argument="--sortfields" type="select" optional="true" multiple="true" label="Fields to sort the results"> <option value="secondary_sample_accession">secondary sample accession number</option> <option value="environment_material">Environment (Material)</option> <option value="host_sex">physical sex of the host</option> <option value="ecotype">a population within a given species displaying traits that reflect adaptation to a local habitat</option> <option value="center_name">Submitting center</option> <option value="serotype">serological variety of a species characterized by its antigenic properties</option> <option value="sex">sex of the organism from which the sample was obtained</option> <option value="host_phenotype">phenotype of host</option> <option value="sampling_site">the site/station where this sample was collection</option> <option value="sequencing_method">sequencing method used</option> <option value="cell_line">cell line from which the sample was obtained</option> <option value="bio_material">identifier for biological material including institute and collection code</option> <option value="target_gene">targeted gene or locus name for marker gene studies</option> <option value="experimental_factor">variable aspects of the experimental design</option> <option value="identified_by">name of the taxonomist who identified the specimen</option> <option value="cell_type">cell type from which the sample was obtained</option> <option value="temperature">Temperature (C)</option> <option value="sampling_platform">the large infrastructure from which this sample was collected</option> <option value="variety">variety (varietas, a formal Linnaean rank) of organism from which sample was derived</option> <option value="collection_date">date that the specimen was collected</option> <option value="specimen_voucher">identifier for the sample culture including institute and collection code</option> <option value="altitude">Altitude (m)</option> <option value="dev_stage">sample obtained from an organism in a specific developmental stage</option> <option value="isolate">individual isolate from which sample was obtained</option> <option value="investigation_type">the study type targeted by the sequencing</option> <option value="serovar">serological variety of a species (usually a prokaryote) characterized by its antigenic properties</option> <option value="protocol_label">the protocol used to produce the sample</option> <option value="location">geographic location of isolation of the sample</option> <option value="host_genotype">genotype of host</option> <option value="ph">pH</option> <option value="broker_name">broker name</option> <option value="germline">the sample is an unrearranged molecule that was inherited from the parental germline</option> <option value="project_name">name of the project within which the sequencing was organized</option> <option value="elevation">Elevation (m)</option> <option value="description">brief sequence description</option> <option value="sample_alias">submitter's name for the sample</option> <option value="checklist">checklist name (or ID)</option> <option value="sampling_campaign">the activity within which this sample was collected</option> <option value="accession">accession number</option> <option value="isolation_source">describes the physical, environmental and/or local geographical source of the sample</option> <option value="mating_type">mating type of the organism from which the sequence was obtained</option> <option value="tissue_type">tissue type from which the sample was obtained</option> <option value="sub_strain">name or identifier of a genetically or otherwise modified strain from which sample was obtained</option> <option value="tissue_lib">tissue library from which sample was obtained</option> <option value="cultivar">cultivar (cultivated variety) of plant from which sample was obtained</option> <option value="environment_biome">Environment (Biome)</option> <option value="environmental_package">MIGS/MIMS/MIMARKS extension for reporting (from environment where the sample was obtained)</option> <option value="sub_species">name of sub-species of organism from which sample was obtained</option> <option value="first_public">date when made public</option> <option value="environment_feature">Environment (Feature)</option> <option value="host">natural (as opposed to laboratory) host to the organism from which sample was obtained</option> <option value="country">locality of sample isolation: country names, oceans or seas, followed by regions and localities</option> <option value="collected_by">name of the person who collected the specimen</option> <option value="environmental_sample">identifies sequences derived by direct molecular isolation from an environmental DNA sample</option> <option value="salinity">Salinity (PSU)</option> <option value="host_status">condition of host (eg. diseased or healthy)</option> <option value="strain">strain from which sample was obtained</option> <option value="depth">Depth (m)</option> <option value="host_tax_id">NCBI taxon id of the host</option> <option value="host_body_site">name of body site from where the sample was obtained</option> <option value="host_growth_conditions">literature reference giving growth conditions of the host</option> <option value="sample_collection">the method or deviced employed for collecting the sample</option> <option value="culture_collection">identifier for the sample culture including institute and collection code</option> </param> </when> <when value="fasta"/> </conditional> </when> <when value="environmental"> <conditional name="display_opt"> <param argument="--display" type="select" label="Display option to specify the display format"> <expand macro="display_options"/> </param> <when value="xml"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> </when> <when value="text"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> </when> <when value="fastq"/> <when value="html"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> </when> <when value="report"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> <param argument="--fields" type="select" multiple="true" label="Fields to return"> <option value="accession">accession</option> <option value="secondary_sample_accession">secondary_sample_accession</option> <option value="bio_material">bio_material</option> <option value="cell_line">cell_line</option> <option value="collected_by">collected_by</option> <option value="collection_date">collection_date</option> <option value="country">country</option> <option value="marine_region">marine_region</option> <option value="cultivar">cultivar</option> <option value="description">description</option> <option value="dev_stage">dev_stage</option> <option value="first_public">first_public</option> <option value="identified_by">identified_by</option> <option value="isolation_source">isolation_source</option> <option value="location">location</option> <option value="strain">strain</option> <option value="tissue_type">tissue_type</option> <option value="tax_id">tax_id</option> <option value="scientific_name">scientific_name</option> <option value="sample_alias">sample_alias</option> <option value="checklist">checklist</option> <option value="center_name">center_name</option> <option value="depth">depth</option> <option value="elevation">elevation</option> <option value="altitude">altitude</option> <option value="environment_biome">environment_biome</option> <option value="environment_feature">environment_feature</option> <option value="environment_material">environment_material</option> <option value="temperature">temperature</option> <option value="salinity">salinity</option> <option value="sampling_campaign">sampling_campaign</option> <option value="sampling_site">sampling_site</option> <option value="sampling_platform">sampling_platform</option> <option value="protocol_label">protocol_label</option> <option value="project_name">project_name</option> <option value="host">host</option> <option value="host_tax_id">host_tax_id</option> <option value="host_status">host_status</option> <option value="host_sex">host_sex</option> <option value="submitted_host_sex">submitted_host_sex</option> <option value="host_body_site">host_body_site</option> <option value="host_gravidity">host_gravidity</option> <option value="host_phenotype">host_phenotype</option> <option value="host_genotype">host_genotype</option> <option value="host_growth_conditions">host_growth_conditions</option> <option value="environmental_package">environmental_package</option> <option value="investigation_type">investigation_type</option> <option value="experimental_factor">experimental_factor</option> <option value="sample_collection">sample_collection</option> <option value="sequencing_method">sequencing_method</option> <option value="target_gene">target_gene</option> <option value="ph">ph</option> <option value="broker_name">broker_name</option> <option value="event_label">event_label</option> </param> <param argument="--sortfields" type="select" optional="true" multiple="true" label="Fields to sort the results"> <option value="secondary_sample_accession">secondary sample accession number</option> <option value="environment_material">Environment (Material)</option> <option value="dev_stage">sample obtained from an organism in a specific developmental stage</option> <option value="event_label">label given to sampling event</option> <option value="center_name">Submitting center</option> <option value="accession">accession number</option> <option value="host_phenotype">phenotype of host</option> <option value="cell_line">cell line from which the sample was obtained</option> <option value="bio_material">identifier for biological material including institute and collection code</option> <option value="target_gene">targeted gene or locus name for marker gene studies</option> <option value="experimental_factor">variable aspects of the experimental design</option> <option value="identified_by">name of the taxonomist who identified the specimen</option> <option value="temperature">Temperature (C)</option> <option value="sampling_platform">the large infrastructure from which this sample was collected</option> <option value="collected_by">name of the person who collected the specimen</option> <option value="collection_date">date that the specimen was collected</option> <option value="altitude">Altitude (m)</option> <option value="host_sex">physical sex of the host</option> <option value="investigation_type">the study type targeted by the sequencing</option> <option value="location">geographic location of isolation of the sample</option> <option value="host_genotype">genotype of host</option> <option value="ph">pH</option> <option value="broker_name">broker name</option> <option value="project_name">name of the project within which the sequencing was organized</option> <option value="elevation">Elevation (m)</option> <option value="description">brief sequence description</option> <option value="sample_alias">submitter's name for the sample</option> <option value="checklist">checklist name (or ID)</option> <option value="sampling_campaign">the activity within which this sample was collected</option> <option value="protocol_label">the protocol used to produce the sample</option> <option value="isolation_source">describes the physical, environmental and/or local geographical source of the sample</option> <option value="sampling_site">the site/station where this sample was collection</option> <option value="host_tax_id">NCBI taxon id of the host</option> <option value="cultivar">cultivar (cultivated variety) of plant from which sample was obtained</option> <option value="environment_biome">Environment (Biome)</option> <option value="environmental_package">MIGS/MIMS/MIMARKS extension for reporting (from environment where the sample was obtained)</option> <option value="marine_region">geographical origin of the sample as defined by the marine region</option> <option value="first_public">date when made public</option> <option value="environment_feature">Environment (Feature)</option> <option value="country">locality of sample isolation: country names, oceans or seas, followed by regions and localities</option> <option value="host">natural (as opposed to laboratory) host to the organism from which sample was obtained</option> <option value="salinity">Salinity (PSU)</option> <option value="host_status">condition of host (eg. diseased or healthy)</option> <option value="strain">strain from which sample was obtained</option> <option value="depth">Depth (m)</option> <option value="tissue_type">tissue type from which the sample was obtained</option> <option value="host_body_site">name of body site from where the sample was obtained</option> <option value="host_growth_conditions">literature reference giving growth conditions of the host</option> <option value="sample_collection">the method or deviced employed for collecting the sample</option> <option value="sequencing_method">sequencing method used</option> </param> </when> <when value="fasta"/> </conditional> </when> <when value="read_run"> <conditional name="display_opt"> <param argument="--display" type="select" label="Display option to specify the display format"> <expand macro="display_options"/> </param> <when value="xml"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> </when> <when value="text"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> </when> <when value="fastq"/> <when value="html"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> </when> <when value="report"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> <param argument="--fields" type="select" multiple="true" label="Fields to return"> <option value="study_accession">study_accession</option> <option value="secondary_study_accession">secondary_study_accession</option> <option value="sample_accession">sample_accession</option> <option value="secondary_sample_accession">secondary_sample_accession</option> <option value="experiment_accession">experiment_accession</option> <option value="run_accession">run_accession</option> <option value="submission_accession">submission_accession</option> <option value="tax_id">tax_id</option> <option value="scientific_name">scientific_name</option> <option value="instrument_platform">instrument_platform</option> <option value="instrument_model">instrument_model</option> <option value="library_name">library_name</option> <option value="nominal_length">nominal_length</option> <option value="library_layout">library_layout</option> <option value="library_strategy">library_strategy</option> <option value="library_source">library_source</option> <option value="library_selection">library_selection</option> <option value="read_count">read_count</option> <option value="base_count">base_count</option> <option value="center_name">center_name</option> <option value="first_public">first_public</option> <option value="last_updated">last_updated</option> <option value="experiment_title">experiment_title</option> <option value="study_title">study_title</option> <option value="study_alias">study_alias</option> <option value="experiment_alias">experiment_alias</option> <option value="run_alias">run_alias</option> <option value="fastq_bytes">fastq_bytes</option> <option value="fastq_md5">fastq_md5</option> <option value="fastq_ftp">fastq_ftp</option> <option value="fastq_aspera">fastq_aspera</option> <option value="fastq_galaxy">fastq_galaxy</option> <option value="submitted_bytes">submitted_bytes</option> <option value="submitted_md5">submitted_md5</option> <option value="submitted_ftp">submitted_ftp</option> <option value="submitted_aspera">submitted_aspera</option> <option value="submitted_galaxy">submitted_galaxy</option> <option value="submitted_format">submitted_format</option> <option value="sra_bytes">sra_bytes</option> <option value="sra_md5">sra_md5</option> <option value="sra_ftp">sra_ftp</option> <option value="sra_aspera">sra_aspera</option> <option value="sra_galaxy">sra_galaxy</option> <option value="cram_index_ftp">cram_index_ftp</option> <option value="cram_index_aspera">cram_index_aspera</option> <option value="cram_index_galaxy">cram_index_galaxy</option> <option value="sample_alias">sample_alias</option> <option value="broker_name">broker_name</option> </param> <param argument="--sortfields" type="select" optional="true" multiple="true" label="Fields to sort the results"> <option value="secondary_sample_accession">secondary sample accession number</option> <option value="library_name">sequencing library name</option> <option value="read_count">number of reads</option> <option value="last_updated">date when last updated</option> <option value="center_name">Submitting center</option> <option value="submission_accession">submission accession number</option> <option value="nominal_length">average fragmentation size of paired reads</option> <option value="base_count">number of base pairs</option> <option value="run_accession">run accession number</option> <option value="library_selection">method used to select or enrich the material being sequenced</option> <option value="library_strategy">sequencing technique intended for the library</option> <option value="experiment_accession">experiment accession number</option> <option value="study_alias">submitter's name for the study</option> <option value="submitted_format"></option> <option value="broker_name">broker name</option> <option value="sample_alias">submitter's name for the sample</option> <option value="run_alias">submitter's name for the run</option> <option value="secondary_study_accession">project accession number</option> <option value="study_accession">study accession number</option> <option value="library_layout">sequencing library layout</option> <option value="library_source">source material being sequenced</option> <option value="experiment_title">brief experiment title</option> <option value="first_public">date when made public</option> <option value="instrument_platform">instrument platform used in sequencing experiment</option> <option value="instrument_model">instrument model used in sequencing experiment</option> <option value="sample_accession">sample accession number</option> <option value="experiment_alias">submitter's name for the experiment</option> <option value="study_title">brief sequencing study description</option> </param> </when> <when value="fasta"/> </conditional> </when> <when value="read_study"> <conditional name="display_opt"> <param argument="--display" type="select" label="Display option to specify the display format"> <expand macro="display_options"/> </param> <when value="xml"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> </when> <when value="text"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> </when> <when value="fastq"/> <when value="html"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> </when> <when value="report"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> <param argument="--fields" type="select" multiple="true" label="Fields to return"> <option value="study_accession">study_accession</option> <option value="secondary_study_accession">secondary_study_accession</option> <option value="study_title">study_title</option> <option value="study_alias">study_alias</option> </param> <param argument="--sortfields" type="select" optional="true" multiple="true" label="Fields to sort the results"> <option value="study_title">brief sequencing study description</option> <option value="secondary_study_accession">project accession number</option> <option value="study_alias">submitter's name for the study</option> <option value="study_accession">study accession number</option> </param> </when> <when value="fasta"/> </conditional> </when> <when value="read_experiment"> <conditional name="display_opt"> <param argument="--display" type="select" label="Display option to specify the display format"> <expand macro="display_options"/> </param> <when value="xml"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> </when> <when value="text"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> </when> <when value="fastq"/> <when value="html"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> </when> <when value="report"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> <param argument="--fields" type="select" multiple="true" label="Fields to return"> <option value="study_accession">study_accession</option> <option value="secondary_study_accession">secondary_study_accession</option> <option value="experiment_accession">experiment_accession</option> <option value="instrument_platform">instrument_platform</option> <option value="instrument_model">instrument_model</option> <option value="library_name">library_name</option> <option value="library_layout">library_layout</option> <option value="library_strategy">library_strategy</option> <option value="library_source">library_source</option> <option value="library_selection">library_selection</option> <option value="experiment_title">experiment_title</option> <option value="study_title">study_title</option> <option value="study_alias">study_alias</option> <option value="experiment_alias">experiment_alias</option> </param> <param argument="--sortfields" type="select" optional="true" multiple="true" label="Fields to sort the results"> <option value="library_name">sequencing library name</option> <option value="study_title">brief sequencing study description</option> <option value="instrument_platform">instrument platform used in sequencing experiment</option> <option value="instrument_model">instrument model used in sequencing experiment</option> <option value="study_alias">submitter's name for the study</option> <option value="experiment_alias">submitter's name for the experiment</option> <option value="secondary_study_accession">project accession number</option> <option value="study_accession">study accession number</option> <option value="library_selection">method used to select or enrich the material being sequenced</option> <option value="library_layout">sequencing library layout</option> <option value="library_strategy">sequencing technique intended for the library</option> <option value="experiment_accession">experiment accession number</option> <option value="library_source">source material being sequenced</option> <option value="experiment_title">brief experiment title</option> </param> </when> <when value="fasta"/> </conditional> </when> <when value="analysis"> <conditional name="display_opt"> <param argument="--display" type="select" label="Display option to specify the display format"> <expand macro="display_options"/> </param> <when value="xml"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> </when> <when value="text"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> </when> <when value="fastq"/> <when value="html"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> </when> <when value="report"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> <param argument="--fields" type="select" multiple="true" label="Fields to return"> <option value="analysis_accession">analysis_accession</option> <option value="study_accession">study_accession</option> <option value="secondary_study_accession">secondary_study_accession</option> <option value="sample_accession">sample_accession</option> <option value="secondary_sample_accession">secondary_sample_accession</option> <option value="analysis_title">analysis_title</option> <option value="analysis_type">analysis_type</option> <option value="center_name">center_name</option> <option value="first_public">first_public</option> <option value="last_updated">last_updated</option> <option value="study_title">study_title</option> <option value="tax_id">tax_id</option> <option value="scientific_name">scientific_name</option> <option value="analysis_alias">analysis_alias</option> <option value="study_alias">study_alias</option> <option value="submitted_bytes">submitted_bytes</option> <option value="submitted_md5">submitted_md5</option> <option value="submitted_ftp">submitted_ftp</option> <option value="submitted_aspera">submitted_aspera</option> <option value="submitted_galaxy">submitted_galaxy</option> <option value="sample_alias">sample_alias</option> <option value="broker_name">broker_name</option> </param> <param argument="--sortfields" type="select" optional="true" multiple="true" label="Fields to sort the results"> <option value="secondary_sample_accession">secondary sample accession number</option> <option value="broker_name">broker name</option> <option value="study_accession">study accession number</option> <option value="last_updated">date when last updated</option> <option value="first_public">date when made public</option> <option value="sample_alias">submitter's name for the sample</option> <option value="center_name">Submitting center</option> <option value="analysis_title">brief sequence analysis description</option> <option value="sample_accession">sample accession number</option> <option value="analysis_accession">analysis accession number</option> <option value="secondary_study_accession">project accession number</option> <option value="analysis_alias">submitter's name for the analysis</option> <option value="analysis_type">type of sequence analysis</option> <option value="study_title">brief sequencing study description</option> <option value="study_alias">submitter's name for the study</option> </param> </when> <when value="fasta"/> </conditional> </when> <when value="sequence_update"> <conditional name="display_opt"> <param argument="--display" type="select" label="Display option to specify the display format"> <expand macro="display_options"/> </param> <when value="xml"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> </when> <when value="text"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> </when> <when value="fastq"/> <when value="html"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> </when> <when value="report"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> <param argument="--fields" type="select" multiple="true" label="Fields to return"> <option value="accession">accession</option> <option value="base_count">base_count</option> <option value="bio_material">bio_material</option> <option value="cell_line">cell_line</option> <option value="cell_type">cell_type</option> <option value="collected_by">collected_by</option> <option value="collection_date">collection_date</option> <option value="country">country</option> <option value="cultivar">cultivar</option> <option value="culture_collection">culture_collection</option> <option value="dataclass">dataclass</option> <option value="description">description</option> <option value="dev_stage">dev_stage</option> <option value="ecotype">ecotype</option> <option value="environmental_sample">environmental_sample</option> <option value="first_public">first_public</option> <option value="germline">germline</option> <option value="host">host</option> <option value="identified_by">identified_by</option> <option value="isolate">isolate</option> <option value="isolation_source">isolation_source</option> <option value="keywords">keywords</option> <option value="lab_host">lab_host</option> <option value="last_updated">last_updated</option> <option value="location">location</option> <option value="mating_type">mating_type</option> <option value="mol_type">mol_type</option> <option value="organelle">organelle</option> <option value="serotype">serotype</option> <option value="serovar">serovar</option> <option value="sex">sex</option> <option value="submitted_sex">submitted_sex</option> <option value="specimen_voucher">specimen_voucher</option> <option value="strain">strain</option> <option value="sub_species">sub_species</option> <option value="sub_strain">sub_strain</option> <option value="tax_division">tax_division</option> <option value="tissue_lib">tissue_lib</option> <option value="tissue_type">tissue_type</option> <option value="topology">topology</option> <option value="variety">variety</option> <option value="tax_id">tax_id</option> <option value="scientific_name">scientific_name</option> <option value="altitude">altitude</option> <option value="haplotype">haplotype</option> <option value="plasmid">plasmid</option> <option value="study_accession">study_accession</option> <option value="sequence_md5">sequence_md5</option> </param> <param argument="--sortfields" type="select" optional="true" multiple="true" label="Fields to sort the results"> <option value="mol_type">in vivo molecule type of the sequence</option> <option value="last_updated">date when last updated</option> <option value="sequence_md5"></option> <option value="haplotype">combination of alleles that are linked together on the same physical chromosome</option> <option value="serotype">serological variety of a species characterized by its antigenic properties</option> <option value="sex">sex of the organism from which the sample was obtained</option> <option value="keywords">keywords associated with sequence</option> <option value="collected_by">name of the person who collected the specimen</option> <option value="cell_line">cell line from which the sample was obtained</option> <option value="ecotype">a population within a given species displaying traits that reflect adaptation to a local habitat</option> <option value="bio_material">identifier for biological material including institute and collection code</option> <option value="identified_by">name of the taxonomist who identified the specimen</option> <option value="cell_type">cell type from which the sample was obtained</option> <option value="lab_host">scientific name of the laboratory host used to propagate the source organism for the sample</option> <option value="tax_division">taxonomic division</option> <option value="collection_date">date that the specimen was collected</option> <option value="specimen_voucher">identifier for the sample culture including institute and collection code</option> <option value="altitude">Altitude (m)</option> <option value="dev_stage">sample obtained from an organism in a specific developmental stage</option> <option value="isolate">individual isolate from which sample was obtained</option> <option value="location">geographic location of isolation of the sample</option> <option value="study_accession">study accession number</option> <option value="germline">the sample is an unrearranged molecule that was inherited from the parental germline</option> <option value="description">brief sequence description</option> <option value="accession">accession number</option> <option value="isolation_source">describes the physical, environmental and/or local geographical source of the sample</option> <option value="mating_type">mating type of the organism from which the sequence was obtained</option> <option value="tissue_type">tissue type from which the sample was obtained</option> <option value="sub_strain">name or identifier of a genetically or otherwise modified strain from which sample was obtained</option> <option value="tissue_lib">tissue library from which sample was obtained</option> <option value="cultivar">cultivar (cultivated variety) of plant from which sample was obtained</option> <option value="base_count">number of base pairs</option> <option value="topology">sequence topology: circular or linear</option> <option value="sub_species">name of sub-species of organism from which sample was obtained</option> <option value="environmental_sample">identifies sequences derived by direct molecular isolation from an environmental DNA sample</option> <option value="first_public">date when made public</option> <option value="strain">strain from which sample was obtained</option> <option value="country">locality of sample isolation: country names, oceans or seas, followed by regions and localities</option> <option value="variety">variety (varietas, a formal Linnaean rank) of organism from which sample was derived</option> <option value="host">natural (as opposed to laboratory) host to the organism from which sample was obtained</option> <option value="organelle">membrane-bound intracellular structure from which the sequence was obtained</option> <option value="serovar">serological variety of a species (usually a prokaryote) characterized by its antigenic properties</option> <option value="plasmid">name of naturally occurring plasmid from which the sequence was obtained</option> <option value="dataclass">sequence data class</option> <option value="culture_collection">identifier for the sample culture including institute and collection code</option> </param> </when> <when value="fasta"/> </conditional> </when> <when value="coding_update"> <conditional name="display_opt"> <param argument="--display" type="select" label="Display option to specify the display format"> <expand macro="display_options"/> </param> <when value="xml"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> </when> <when value="text"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> </when> <when value="fastq"/> <when value="html"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> </when> <when value="report"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> <param argument="--fields" type="select" multiple="true" label="Fields to return"> <option value="accession">accession</option> <option value="base_count">base_count</option> <option value="bio_material">bio_material</option> <option value="cell_line">cell_line</option> <option value="cell_type">cell_type</option> <option value="collected_by">collected_by</option> <option value="collection_date">collection_date</option> <option value="country">country</option> <option value="cultivar">cultivar</option> <option value="culture_collection">culture_collection</option> <option value="dataclass">dataclass</option> <option value="description">description</option> <option value="dev_stage">dev_stage</option> <option value="ecotype">ecotype</option> <option value="environmental_sample">environmental_sample</option> <option value="first_public">first_public</option> <option value="germline">germline</option> <option value="host">host</option> <option value="identified_by">identified_by</option> <option value="isolate">isolate</option> <option value="isolation_source">isolation_source</option> <option value="keywords">keywords</option> <option value="lab_host">lab_host</option> <option value="last_updated">last_updated</option> <option value="location">location</option> <option value="mating_type">mating_type</option> <option value="mol_type">mol_type</option> <option value="organelle">organelle</option> <option value="serotype">serotype</option> <option value="serovar">serovar</option> <option value="sex">sex</option> <option value="submitted_sex">submitted_sex</option> <option value="specimen_voucher">specimen_voucher</option> <option value="strain">strain</option> <option value="sub_species">sub_species</option> <option value="sub_strain">sub_strain</option> <option value="tax_division">tax_division</option> <option value="tissue_lib">tissue_lib</option> <option value="tissue_type">tissue_type</option> <option value="variety">variety</option> <option value="allele">allele</option> <option value="artificial_location">artificial_location</option> <option value="codon_start">codon_start</option> <option value="ec_number">ec_number</option> <option value="exception">exception</option> <option value="experiment">experiment</option> <option value="function">function</option> <option value="topology">topology</option> <option value="gene">gene</option> <option value="gene_synonym">gene_synonym</option> <option value="inference">inference</option> <option value="locus_tag">locus_tag</option> <option value="map">map</option> <option value="note">note</option> <option value="old_locus_tag">old_locus_tag</option> <option value="operon">operon</option> <option value="partial">partial</option> <option value="product">product</option> <option value="protein_id">protein_id</option> <option value="pseudo">pseudo</option> <option value="pseudo_gene">pseudo_gene</option> <option value="ribosomal_slippage">ribosomal_slippage</option> <option value="standard_name">standard_name</option> <option value="trans_splicing">trans_splicing</option> <option value="transl_except">transl_except</option> <option value="transl_table">transl_table</option> <option value="tax_id">tax_id</option> <option value="scientific_name">scientific_name</option> <option value="parent_accession">parent_accession</option> <option value="altitude">altitude</option> <option value="haplotype">haplotype</option> <option value="sequence_md5">sequence_md5</option> </param> <param argument="--sortfields" type="select" optional="true" multiple="true" label="Fields to sort the results"> <option value="operon">name of the group of contiguous genes transcribed into a single transcript</option> <option value="mol_type">in vivo molecule type of the sequence</option> <option value="last_updated">date when last updated</option> <option value="lab_host">scientific name of the laboratory host used to propagate the source organism for the sample</option> <option value="transl_except">a single codon translation that does not conform to genetic code</option> <option value="haplotype">combination of alleles that are linked together on the same physical chromosome</option> <option value="serotype">serological variety of a species characterized by its antigenic properties</option> <option value="trans_splicing">indicates exons from two RNA molecules are ligated in intermolecular reaction to form mature RNA</option> <option value="sex">sex of the organism from which the sample was obtained</option> <option value="pseudo_gene">indicates that this feature is a pseudogene</option> <option value="standard_name">accepted standard name for a feature</option> <option value="collected_by">name of the person who collected the specimen</option> <option value="germline">the sample is an unrearranged molecule that was inherited from the parental germline</option> <option value="cell_type">cell type from which the sample was obtained</option> <option value="host">natural (as opposed to laboratory) host to the organism from which sample was obtained</option> <option value="inference">a structured description of non-experimental evidence</option> <option value="bio_material">identifier for biological material including institute and collection code</option> <option value="parent_accession">parent sequence accession number</option> <option value="identified_by">name of the taxonomist who identified the specimen</option> <option value="locus_tag">a submitter-supplied, systematic, stable identifier for a gene and its associated features</option> <option value="sequence_md5"></option> <option value="tax_division">taxonomic division</option> <option value="old_locus_tag">deprecated submitter-supplied, systematic, stable identifier for a gene and its associated features</option> <option value="specimen_voucher">identifier for the sample culture including institute and collection code</option> <option value="altitude">Altitude (m)</option> <option value="dev_stage">sample obtained from an organism in a specific developmental stage</option> <option value="isolate">individual isolate from which sample was obtained</option> <option value="ec_number">Enzyme Commission number for enzyme product of sequence</option> <option value="note">any comment or additional information</option> <option value="experiment">a brief description of the nature of the experimental evidence</option> <option value="location">geographic location of isolation of the sample</option> <option value="collection_date">date that the specimen was collected</option> <option value="allele">name of the allele for the given gene</option> <option value="protein_id">a stable protein identifier issued by INSDC</option> <option value="partial">differentiates between complete regions and partial ones (deprecated qualifier)</option> <option value="artificial_location">indicates location is modified to adjust for the presence of a frameshift or internal stop codon</option> <option value="function">function attributed to a sequence</option> <option value="map">genomic map position of feature</option> <option value="product">name of the product associated with the feature</option> <option value="description">brief sequence description</option> <option value="cell_line">cell line from which the sample was obtained</option> <option value="gene_synonym">synonymous, replaced, obsolete or former gene symbol</option> <option value="ecotype">a population within a given species displaying traits that reflect adaptation to a local habitat</option> <option value="exception">indicates that the coding region cannot be translated using standard biological rules</option> <option value="accession">accession number</option> <option value="isolation_source">describes the physical, environmental and/or local geographical source of the sample</option> <option value="mating_type">mating type of the organism from which the sequence was obtained</option> <option value="tissue_type">tissue type from which the sample was obtained</option> <option value="sub_strain">name or identifier of a genetically or otherwise modified strain from which sample was obtained</option> <option value="tissue_lib">tissue library from which sample was obtained</option> <option value="cultivar">cultivar (cultivated variety) of plant from which sample was obtained</option> <option value="base_count">number of base pairs</option> <option value="topology">sequence topology: circular or linear</option> <option value="sub_species">name of sub-species of organism from which sample was obtained</option> <option value="first_public">date when made public</option> <option value="strain">strain from which sample was obtained</option> <option value="country">locality of sample isolation: country names, oceans or seas, followed by regions and localities</option> <option value="variety">variety (varietas, a formal Linnaean rank) of organism from which sample was derived</option> <option value="pseudo">the feature is non-functional</option> <option value="environmental_sample">identifies sequences derived by direct molecular isolation from an environmental DNA sample</option> <option value="transl_table">indicates the genetic code table used if other than universal genetic code table</option> <option value="organelle">membrane-bound intracellular structure from which the sequence was obtained</option> <option value="ribosomal_slippage">indicates ribosomal slippage (change to an alternative reading frame) during protein translation</option> <option value="serovar">serological variety of a species (usually a prokaryote) characterized by its antigenic properties</option> <option value="keywords">keywords associated with sequence</option> <option value="dataclass">sequence data class</option> <option value="gene">symbol of the gene corresponding to a sequence region</option> <option value="codon_start">indicates the offset of the first complete codon relative to the first base of the coding feature</option> <option value="culture_collection">identifier for the sample culture including institute and collection code</option> </param> </when> <when value="fasta"/> </conditional> </when> <when value="tsa_set"> <conditional name="display_opt"> <param argument="--display" type="select" label="Display option to specify the display format"> <expand macro="display_options"/> </param> <when value="xml"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> </when> <when value="text"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> </when> <when value="fastq"/> <when value="html"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> </when> <when value="report"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> <param argument="--fields" type="select" multiple="true" label="Fields to return"> <option value="accession">accession</option> <option value="bio_material">bio_material</option> <option value="cell_line">cell_line</option> <option value="cell_type">cell_type</option> <option value="collected_by">collected_by</option> <option value="collection_date">collection_date</option> <option value="country">country</option> <option value="cultivar">cultivar</option> <option value="culture_collection">culture_collection</option> <option value="description">description</option> <option value="dev_stage">dev_stage</option> <option value="ecotype">ecotype</option> <option value="environmental_sample">environmental_sample</option> <option value="first_public">first_public</option> <option value="germline">germline</option> <option value="host">host</option> <option value="identified_by">identified_by</option> <option value="isolate">isolate</option> <option value="isolation_source">isolation_source</option> <option value="keywords">keywords</option> <option value="lab_host">lab_host</option> <option value="last_updated">last_updated</option> <option value="location">location</option> <option value="mating_type">mating_type</option> <option value="mol_type">mol_type</option> <option value="serotype">serotype</option> <option value="serovar">serovar</option> <option value="sex">sex</option> <option value="submitted_sex">submitted_sex</option> <option value="specimen_voucher">specimen_voucher</option> <option value="strain">strain</option> <option value="sub_species">sub_species</option> <option value="sub_strain">sub_strain</option> <option value="tax_division">tax_division</option> <option value="tissue_lib">tissue_lib</option> <option value="tissue_type">tissue_type</option> <option value="variety">variety</option> <option value="tax_id">tax_id</option> <option value="scientific_name">scientific_name</option> <option value="altitude">altitude</option> <option value="haplotype">haplotype</option> <option value="study_accession">study_accession</option> <option value="set_files">set_files</option> </param> <param argument="--sortfields" type="select" optional="true" multiple="true" label="Fields to sort the results"> <option value="mol_type">in vivo molecule type of the sequence</option> <option value="last_updated">date when last updated</option> <option value="lab_host">scientific name of the laboratory host used to propagate the source organism for the sample</option> <option value="haplotype">combination of alleles that are linked together on the same physical chromosome</option> <option value="accession">accession number</option> <option value="sex">sex of the organism from which the sample was obtained</option> <option value="cell_line">cell line from which the sample was obtained</option> <option value="host">natural (as opposed to laboratory) host to the organism from which sample was obtained</option> <option value="ecotype">a population within a given species displaying traits that reflect adaptation to a local habitat</option> <option value="bio_material">identifier for biological material including institute and collection code</option> <option value="identified_by">name of the taxonomist who identified the specimen</option> <option value="cell_type">cell type from which the sample was obtained</option> <option value="tax_division">taxonomic division</option> <option value="collection_date">date that the specimen was collected</option> <option value="specimen_voucher">identifier for the sample culture including institute and collection code</option> <option value="altitude">Altitude (m)</option> <option value="dev_stage">sample obtained from an organism in a specific developmental stage</option> <option value="isolate">individual isolate from which sample was obtained</option> <option value="location">geographic location of isolation of the sample</option> <option value="study_accession">study accession number</option> <option value="germline">the sample is an unrearranged molecule that was inherited from the parental germline</option> <option value="description">brief sequence description</option> <option value="tissue_lib">tissue library from which sample was obtained</option> <option value="isolation_source">describes the physical, environmental and/or local geographical source of the sample</option> <option value="mating_type">mating type of the organism from which the sequence was obtained</option> <option value="serovar">serological variety of a species (usually a prokaryote) characterized by its antigenic properties</option> <option value="serotype">serological variety of a species characterized by its antigenic properties</option> <option value="sub_strain">name or identifier of a genetically or otherwise modified strain from which sample was obtained</option> <option value="cultivar">cultivar (cultivated variety) of plant from which sample was obtained</option> <option value="collected_by">name of the person who collected the specimen</option> <option value="sub_species">name of sub-species of organism from which sample was obtained</option> <option value="first_public">date when made public</option> <option value="strain">strain from which sample was obtained</option> <option value="country">locality of sample isolation: country names, oceans or seas, followed by regions and localities</option> <option value="variety">variety (varietas, a formal Linnaean rank) of organism from which sample was derived</option> <option value="environmental_sample">identifies sequences derived by direct molecular isolation from an environmental DNA sample</option> <option value="tissue_type">tissue type from which the sample was obtained</option> <option value="keywords">keywords associated with sequence</option> <option value="culture_collection">identifier for the sample culture including institute and collection code</option> </param> </when> <when value="fasta"/> </conditional> </when> <when value="analysis_study"> <conditional name="display_opt"> <param argument="--display" type="select" label="Display option to specify the display format"> <expand macro="display_options"/> </param> <when value="xml"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> </when> <when value="text"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> </when> <when value="fastq"/> <when value="html"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> </when> <when value="report"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> <param argument="--fields" type="select" multiple="true" label="Fields to return"> <option value="study_accession">study_accession</option> <option value="secondary_study_accession">secondary_study_accession</option> <option value="study_title">study_title</option> <option value="study_alias">study_alias</option> </param> <param argument="--sortfields" type="select" optional="true" multiple="true" label="Fields to sort the results"> <option value="study_title">brief sequencing study description</option> <option value="secondary_study_accession">project accession number</option> <option value="study_alias">submitter's name for the study</option> <option value="study_accession">study accession number</option> </param> </when> <when value="fasta"/> </conditional> </when> <when value="noncoding_update"> <conditional name="display_opt"> <param argument="--display" type="select" label="Display option to specify the display format"> <expand macro="display_options"/> </param> <when value="xml"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> </when> <when value="text"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> </when> <when value="fastq"/> <when value="html"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> </when> <when value="report"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> <param argument="--fields" type="select" multiple="true" label="Fields to return"> <option value="accession">accession</option> <option value="base_count">base_count</option> <option value="collected_by">collected_by</option> <option value="dataclass">dataclass</option> <option value="first_public">first_public</option> <option value="last_updated">last_updated</option> <option value="location">location</option> <option value="tax_division">tax_division</option> <option value="tax_id">tax_id</option> <option value="scientific_name">scientific_name</option> <option value="rna_class">rna_class</option> <option value="gene">gene</option> <option value="gene_synonym">gene_synonym</option> <option value="product">product</option> <option value="anticodon">anticodon</option> <option value="function">function</option> <option value="locus_tag">locus_tag</option> <option value="experiment">experiment</option> <option value="inference">inference</option> <option value="note">note</option> <option value="bio_material">bio_material</option> <option value="cell_line">cell_line</option> <option value="cell_type">cell_type</option> <option value="country">country</option> <option value="cultivar">cultivar</option> <option value="culture_collection">culture_collection</option> <option value="description">description</option> <option value="dev_stage">dev_stage</option> <option value="ecotype">ecotype</option> <option value="environmental_sample">environmental_sample</option> <option value="germline">germline</option> <option value="host">host</option> <option value="identified_by">identified_by</option> <option value="isolate">isolate</option> <option value="isolation_source">isolation_source</option> <option value="keywords">keywords</option> <option value="lab_host">lab_host</option> <option value="mating_type">mating_type</option> <option value="mol_type">mol_type</option> <option value="organelle">organelle</option> <option value="serotype">serotype</option> <option value="serovar">serovar</option> <option value="sex">sex</option> <option value="collection_date">collection_date</option> <option value="submitted_sex">submitted_sex</option> <option value="specimen_voucher">specimen_voucher</option> <option value="strain">strain</option> <option value="sub_species">sub_species</option> <option value="sub_strain">sub_strain</option> <option value="tissue_lib">tissue_lib</option> <option value="tissue_type">tissue_type</option> <option value="topology">topology</option> <option value="variety">variety</option> <option value="sequence_md5">sequence_md5</option> <option value="study_accession">study_accession</option> </param> <param argument="--sortfields" type="select" optional="true" multiple="true" label="Fields to sort the results"> <option value="mol_type">in vivo molecule type of the sequence</option> <option value="last_updated">date when last updated</option> <option value="sequence_md5"></option> <option value="collected_by">name of the person who collected the specimen</option> <option value="serotype">serological variety of a species characterized by its antigenic properties</option> <option value="sex">sex of the organism from which the sample was obtained</option> <option value="keywords">keywords associated with sequence</option> <option value="cell_line">cell line from which the sample was obtained</option> <option value="inference">a structured description of non-experimental evidence</option> <option value="bio_material">identifier for biological material including institute and collection code</option> <option value="identified_by">name of the taxonomist who identified the specimen</option> <option value="note">any comment or additional information</option> <option value="locus_tag">a submitter-supplied, systematic, stable identifier for a gene and its associated features</option> <option value="lab_host">scientific name of the laboratory host used to propagate the source organism for the sample</option> <option value="tax_division">taxonomic division</option> <option value="collection_date">date that the specimen was collected</option> <option value="specimen_voucher">identifier for the sample culture including institute and collection code</option> <option value="dev_stage">sample obtained from an organism in a specific developmental stage</option> <option value="isolate">individual isolate from which sample was obtained</option> <option value="anticodon">location of the anticodon of tRNA and the amino acid for which it codes</option> <option value="experiment">a brief description of the nature of the experimental evidence</option> <option value="location">geographic location of isolation of the sample</option> <option value="study_accession">study accession number</option> <option value="function">function attributed to a sequence</option> <option value="germline">the sample is an unrearranged molecule that was inherited from the parental germline</option> <option value="product">name of the product associated with the feature</option> <option value="description">brief sequence description</option> <option value="ecotype">a population within a given species displaying traits that reflect adaptation to a local habitat</option> <option value="cell_type">cell type from which the sample was obtained</option> <option value="accession">accession number</option> <option value="isolation_source">describes the physical, environmental and/or local geographical source of the sample</option> <option value="mating_type">mating type of the organism from which the sequence was obtained</option> <option value="tissue_type">tissue type from which the sample was obtained</option> <option value="sub_strain">name or identifier of a genetically or otherwise modified strain from which sample was obtained</option> <option value="tissue_lib">tissue library from which sample was obtained</option> <option value="cultivar">cultivar (cultivated variety) of plant from which sample was obtained</option> <option value="base_count">number of base pairs</option> <option value="topology">sequence topology: circular or linear</option> <option value="sub_species">name of sub-species of organism from which sample was obtained</option> <option value="environmental_sample">identifies sequences derived by direct molecular isolation from an environmental DNA sample</option> <option value="first_public">date when made public</option> <option value="strain">strain from which sample was obtained</option> <option value="country">locality of sample isolation: country names, oceans or seas, followed by regions and localities</option> <option value="variety">variety (varietas, a formal Linnaean rank) of organism from which sample was derived</option> <option value="host">natural (as opposed to laboratory) host to the organism from which sample was obtained</option> <option value="gene_synonym">synonymous, replaced, obsolete or former gene symbol</option> <option value="organelle">membrane-bound intracellular structure from which the sequence was obtained</option> <option value="serovar">serological variety of a species (usually a prokaryote) characterized by its antigenic properties</option> <option value="rna_class">classification of RNA</option> <option value="dataclass">sequence data class</option> <option value="gene">symbol of the gene corresponding to a sequence region</option> <option value="culture_collection">identifier for the sample culture including institute and collection code</option> </param> </when> <when value="fasta"/> </conditional> </when> </conditional> </xml> <xml name="conditional_text_search"> <conditional name="res"> <param argument="--result" type="select" label="Result to return"> <option value="noncoding_release">Non-coding sequences (Release)</option> <option value="assembly">Genome assemblies</option> <option value="sequence_release">Nucleotide sequences (Release)</option> <option value="wgs_set">Genome assembly contig set</option> <option value="study">Studies</option> <option value="taxon">Taxonomic classification</option> <option value="coding_release">Protein-coding sequences (Release)</option> <option value="sample">Samples</option> <option value="environmental">Environmental samples</option> <option value="read_run">Raw reads</option> <option value="read_study">Raw reads (grouped by study)</option> <option value="read_experiment">Raw reads (grouped by experiment)</option> <option value="analysis">Nucleotide sequence analyses from reads</option> <option value="sequence_update">Nucleotide sequences (Update)</option> <option value="coding_update">Protein-coding sequences (Update)</option> <option value="tsa_set">Transcriptome assembly contig set</option> <option value="analysis_study">Nucleotide sequence analyses from reads (grouped by study)</option> <option value="noncoding_update">Non-coding sequences (Update)</option> </param> <when value="noncoding_release"> <repeat name="queries" title="Add a query"> <param name="combination_operation" type="select" label="Combination operation"> <option value="AND">AND</option> <option value="OR">OR</option> <option value="NOT">NOT</option> </param> <conditional name="filter_field"> <param name="field" type="select" label="Field to query"> <option value="mol_type">in vivo molecule type of the sequence</option> <option value="last_updated">date when last updated</option> <option value="sequence_md5"></option> <option value="collected_by">name of the person who collected the specimen</option> <option value="serotype">serological variety of a species characterized by its antigenic properties</option> <option value="sex">sex of the organism from which the sample was obtained</option> <option value="keywords">keywords associated with sequence</option> <option value="cell_line">cell line from which the sample was obtained</option> <option value="inference">a structured description of non-experimental evidence</option> <option value="bio_material">identifier for biological material including institute and collection code</option> <option value="identified_by">name of the taxonomist who identified the specimen</option> <option value="note">any comment or additional information</option> <option value="locus_tag">a submitter-supplied, systematic, stable identifier for a gene and its associated features</option> <option value="lab_host">scientific name of the laboratory host used to propagate the source organism for the sample</option> <option value="tax_division">taxonomic division</option> <option value="collection_date">date that the specimen was collected</option> <option value="specimen_voucher">identifier for the sample culture including institute and collection code</option> <option value="dev_stage">sample obtained from an organism in a specific developmental stage</option> <option value="isolate">individual isolate from which sample was obtained</option> <option value="anticodon">location of the anticodon of tRNA and the amino acid for which it codes</option> <option value="experiment">a brief description of the nature of the experimental evidence</option> <option value="location">geographic location of isolation of the sample</option> <option value="study_accession">study accession number</option> <option value="function">function attributed to a sequence</option> <option value="germline">the sample is an unrearranged molecule that was inherited from the parental germline</option> <option value="product">name of the product associated with the feature</option> <option value="description">brief sequence description</option> <option value="ecotype">a population within a given species displaying traits that reflect adaptation to a local habitat</option> <option value="cell_type">cell type from which the sample was obtained</option> <option value="accession">accession number</option> <option value="isolation_source">describes the physical, environmental and/or local geographical source of the sample</option> <option value="mating_type">mating type of the organism from which the sequence was obtained</option> <option value="tissue_type">tissue type from which the sample was obtained</option> <option value="sub_strain">name or identifier of a genetically or otherwise modified strain from which sample was obtained</option> <option value="tissue_lib">tissue library from which sample was obtained</option> <option value="cultivar">cultivar (cultivated variety) of plant from which sample was obtained</option> <option value="base_count">number of base pairs</option> <option value="topology">sequence topology: circular or linear</option> <option value="sub_species">name of sub-species of organism from which sample was obtained</option> <option value="environmental_sample">identifies sequences derived by direct molecular isolation from an environmental DNA sample</option> <option value="first_public">date when made public</option> <option value="strain">strain from which sample was obtained</option> <option value="country">locality of sample isolation: country names, oceans or seas, followed by regions and localities</option> <option value="variety">variety (varietas, a formal Linnaean rank) of organism from which sample was derived</option> <option value="host">natural (as opposed to laboratory) host to the organism from which sample was obtained</option> <option value="gene_synonym">synonymous, replaced, obsolete or former gene symbol</option> <option value="organelle">membrane-bound intracellular structure from which the sequence was obtained</option> <option value="serovar">serological variety of a species (usually a prokaryote) characterized by its antigenic properties</option> <option value="rna_class">classification of RNA</option> <option value="dataclass">sequence data class</option> <option value="gene">symbol of the gene corresponding to a sequence region</option> <option value="culture_collection">identifier for the sample culture including institute and collection code</option> </param> <when value="mol_type"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/> </when> <when value="last_updated"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> <option value="lower">lower</option> <option value="equal or lower">equal or lower</option> <option value="higher">higher</option> <option value="equal or higher">equal or higher</option> </param> <param name="value" type="text" value="" label="A date in the format YYYY-MM-DD"/> </when> <when value="sequence_md5"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="collected_by"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="serotype"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="sex"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/> </when> <when value="keywords"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="cell_line"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="inference"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="bio_material"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="identified_by"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="note"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="locus_tag"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="lab_host"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="tax_division"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/> </when> <when value="collection_date"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> <option value="lower">lower</option> <option value="equal or lower">equal or lower</option> <option value="higher">higher</option> <option value="equal or higher">equal or higher</option> </param> <param name="value" type="text" value="" label="A date in the format YYYY-MM-DD"/> </when> <when value="specimen_voucher"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="dev_stage"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="isolate"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="anticodon"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="experiment"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="location"> <conditional name="op"> <param name="operation" type="select" label="Operation"> <option value="geo_box2">All locations within a box defined by a centre point and a radius in km.</option> <option value="geo_box1">All locations within a box defined by the lower left (SW) and upper right (NE) points.</option> <option value="geo_circ">All locations within a circle defined by a centre point and a radius in km.</option> <option value="geo_lat">All locations within a latitude range given by a latitude and a radius in km.</option> <option value="geo_south">All locations south of a given latitude (inclusive).</option> <option value="geo_point">An exact lat/lon position</option> <option value="geo_north">All locations north of a given latitude (inclusive).</option> </param> <when value="geo_box2"> <param name="values" type="text" value="" label="latitude, longitude, radius (km)" help="Values separated by simple comma"/> </when> <when value="geo_box1"> <param name="values" type="text" value="" label="south-west latitude, south-west longitude, north-east latitude, north-east longitude" help="Values separated by simple comma"/> </when> <when value="geo_circ"> <param name="values" type="text" value="" label="latitude, longitude, radius (km)" help="Values separated by simple comma"/> </when> <when value="geo_lat"> <param name="values" type="text" value="" label="latitude, radius (km)" help="Values separated by simple comma"/> </when> <when value="geo_south"> <param name="values" type="text" value="" label="latitude" help="Values separated by simple comma"/> </when> <when value="geo_point"> <param name="values" type="text" value="" label="latitude, longitude" help="Values separated by simple comma"/> </when> <when value="geo_north"> <param name="values" type="text" value="" label="latitude" help="Values separated by simple comma"/> </when> </conditional> </when> <when value="study_accession"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="function"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="germline"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> </param> <param name="value" type="select" label="Value"> <option value="yes">yes</option> <option value="true">true</option> <option value="no">no</option> <option value="false">false</option> </param> </when> <when value="product"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="description"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="ecotype"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="cell_type"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="accession"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="isolation_source"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="mating_type"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="tissue_type"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="sub_strain"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="tissue_lib"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="cultivar"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="base_count"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> <option value="lower">lower</option> <option value="equal or lower">equal or lower</option> <option value="higher">higher</option> <option value="equal or higher">equal or higher</option> </param> <param name="value" type="float" value="" label="Any integer"/> </when> <when value="topology"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/> </when> <when value="sub_species"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="environmental_sample"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> </param> <param name="value" type="select" label="Value"> <option value="yes">yes</option> <option value="true">true</option> <option value="no">no</option> <option value="false">false</option> </param> </when> <when value="first_public"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> <option value="lower">lower</option> <option value="equal or lower">equal or lower</option> <option value="higher">higher</option> <option value="equal or higher">equal or higher</option> </param> <param name="value" type="text" value="" label="A date in the format YYYY-MM-DD"/> </when> <when value="strain"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="country"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="variety"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="host"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="gene_synonym"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="organelle"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/> </when> <when value="serovar"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="rna_class"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/> </when> <when value="dataclass"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/> </when> <when value="gene"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="culture_collection"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> </conditional> </repeat> <conditional name="display_opt"> <param argument="--display" type="select" label="Display option to specify the display format"> <expand macro="display_options"/> </param> <when value="xml"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> </when> <when value="text"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> </when> <when value="fastq"/> <when value="html"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> </when> <when value="report"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> <param argument="--fields" type="select" multiple="true" label="Fields to return"> <option value="accession">accession</option> <option value="base_count">base_count</option> <option value="collected_by">collected_by</option> <option value="dataclass">dataclass</option> <option value="first_public">first_public</option> <option value="last_updated">last_updated</option> <option value="location">location</option> <option value="tax_division">tax_division</option> <option value="tax_id">tax_id</option> <option value="scientific_name">scientific_name</option> <option value="rna_class">rna_class</option> <option value="gene">gene</option> <option value="gene_synonym">gene_synonym</option> <option value="product">product</option> <option value="anticodon">anticodon</option> <option value="function">function</option> <option value="locus_tag">locus_tag</option> <option value="experiment">experiment</option> <option value="inference">inference</option> <option value="note">note</option> <option value="bio_material">bio_material</option> <option value="cell_line">cell_line</option> <option value="cell_type">cell_type</option> <option value="country">country</option> <option value="cultivar">cultivar</option> <option value="culture_collection">culture_collection</option> <option value="description">description</option> <option value="dev_stage">dev_stage</option> <option value="ecotype">ecotype</option> <option value="environmental_sample">environmental_sample</option> <option value="germline">germline</option> <option value="host">host</option> <option value="identified_by">identified_by</option> <option value="isolate">isolate</option> <option value="isolation_source">isolation_source</option> <option value="keywords">keywords</option> <option value="lab_host">lab_host</option> <option value="mating_type">mating_type</option> <option value="mol_type">mol_type</option> <option value="organelle">organelle</option> <option value="serotype">serotype</option> <option value="serovar">serovar</option> <option value="sex">sex</option> <option value="collection_date">collection_date</option> <option value="submitted_sex">submitted_sex</option> <option value="specimen_voucher">specimen_voucher</option> <option value="strain">strain</option> <option value="sub_species">sub_species</option> <option value="sub_strain">sub_strain</option> <option value="tissue_lib">tissue_lib</option> <option value="tissue_type">tissue_type</option> <option value="topology">topology</option> <option value="variety">variety</option> <option value="sequence_md5">sequence_md5</option> <option value="study_accession">study_accession</option> </param> <param argument="--sortfields" type="select" optional="true" multiple="true" label="Fields to sort the results"> <option value="mol_type">in vivo molecule type of the sequence</option> <option value="last_updated">date when last updated</option> <option value="sequence_md5"></option> <option value="collected_by">name of the person who collected the specimen</option> <option value="serotype">serological variety of a species characterized by its antigenic properties</option> <option value="sex">sex of the organism from which the sample was obtained</option> <option value="keywords">keywords associated with sequence</option> <option value="cell_line">cell line from which the sample was obtained</option> <option value="inference">a structured description of non-experimental evidence</option> <option value="bio_material">identifier for biological material including institute and collection code</option> <option value="identified_by">name of the taxonomist who identified the specimen</option> <option value="note">any comment or additional information</option> <option value="locus_tag">a submitter-supplied, systematic, stable identifier for a gene and its associated features</option> <option value="lab_host">scientific name of the laboratory host used to propagate the source organism for the sample</option> <option value="tax_division">taxonomic division</option> <option value="collection_date">date that the specimen was collected</option> <option value="specimen_voucher">identifier for the sample culture including institute and collection code</option> <option value="dev_stage">sample obtained from an organism in a specific developmental stage</option> <option value="isolate">individual isolate from which sample was obtained</option> <option value="anticodon">location of the anticodon of tRNA and the amino acid for which it codes</option> <option value="experiment">a brief description of the nature of the experimental evidence</option> <option value="location">geographic location of isolation of the sample</option> <option value="study_accession">study accession number</option> <option value="function">function attributed to a sequence</option> <option value="germline">the sample is an unrearranged molecule that was inherited from the parental germline</option> <option value="product">name of the product associated with the feature</option> <option value="description">brief sequence description</option> <option value="ecotype">a population within a given species displaying traits that reflect adaptation to a local habitat</option> <option value="cell_type">cell type from which the sample was obtained</option> <option value="accession">accession number</option> <option value="isolation_source">describes the physical, environmental and/or local geographical source of the sample</option> <option value="mating_type">mating type of the organism from which the sequence was obtained</option> <option value="tissue_type">tissue type from which the sample was obtained</option> <option value="sub_strain">name or identifier of a genetically or otherwise modified strain from which sample was obtained</option> <option value="tissue_lib">tissue library from which sample was obtained</option> <option value="cultivar">cultivar (cultivated variety) of plant from which sample was obtained</option> <option value="base_count">number of base pairs</option> <option value="topology">sequence topology: circular or linear</option> <option value="sub_species">name of sub-species of organism from which sample was obtained</option> <option value="environmental_sample">identifies sequences derived by direct molecular isolation from an environmental DNA sample</option> <option value="first_public">date when made public</option> <option value="strain">strain from which sample was obtained</option> <option value="country">locality of sample isolation: country names, oceans or seas, followed by regions and localities</option> <option value="variety">variety (varietas, a formal Linnaean rank) of organism from which sample was derived</option> <option value="host">natural (as opposed to laboratory) host to the organism from which sample was obtained</option> <option value="gene_synonym">synonymous, replaced, obsolete or former gene symbol</option> <option value="organelle">membrane-bound intracellular structure from which the sequence was obtained</option> <option value="serovar">serological variety of a species (usually a prokaryote) characterized by its antigenic properties</option> <option value="rna_class">classification of RNA</option> <option value="dataclass">sequence data class</option> <option value="gene">symbol of the gene corresponding to a sequence region</option> <option value="culture_collection">identifier for the sample culture including institute and collection code</option> </param> </when> <when value="fasta"/> </conditional> </when> <when value="assembly"> <repeat name="queries" title="Add a query"> <param name="combination_operation" type="select" label="Combination operation"> <option value="AND">AND</option> <option value="OR">OR</option> <option value="NOT">NOT</option> </param> <conditional name="filter_field"> <param name="field" type="select" label="Field to query"> <option value="assembly_name">genome assembly name for all live versions</option> <option value="base_count">number of base pairs</option> <option value="strain">strain from which sample was obtained</option> <option value="study_description">detailed sequencing study description</option> <option value="accession">accession number</option> <option value="assembly_level">assembly level</option> <option value="sample_accession">sample accession number</option> <option value="assembly_title">brief genome assembly description</option> <option value="study_title">brief sequencing study description</option> <option value="genome_representation">whether this is a full or partial genome</option> <option value="study_name">sequencing study name</option> <option value="study_accession">study accession number</option> </param> <when value="assembly_name"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="base_count"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> <option value="lower">lower</option> <option value="equal or lower">equal or lower</option> <option value="higher">higher</option> <option value="equal or higher">equal or higher</option> </param> <param name="value" type="float" value="" label="Any integer"/> </when> <when value="strain"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="study_description"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="accession"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="assembly_level"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/> </when> <when value="sample_accession"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="assembly_title"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="study_title"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="genome_representation"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/> </when> <when value="study_name"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="study_accession"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> </conditional> </repeat> <conditional name="display_opt"> <param argument="--display" type="select" label="Display option to specify the display format"> <expand macro="display_options"/> </param> <when value="xml"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> </when> <when value="text"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> </when> <when value="fastq"/> <when value="html"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> </when> <when value="report"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> <param argument="--fields" type="select" multiple="true" label="Fields to return"> <option value="accession">accession</option> <option value="study_accession">study_accession</option> <option value="sample_accession">sample_accession</option> <option value="assembly_name">assembly_name</option> <option value="assembly_title">assembly_title</option> <option value="study_name">study_name</option> <option value="study_title">study_title</option> <option value="study_description">study_description</option> <option value="tax_id">tax_id</option> <option value="scientific_name">scientific_name</option> <option value="strain">strain</option> <option value="base_count">base_count</option> <option value="assembly_level">assembly_level</option> <option value="genome_representation">genome_representation</option> </param> <param argument="--sortfields" type="select" optional="true" multiple="true" label="Fields to sort the results"> <option value="assembly_name">genome assembly name for all live versions</option> <option value="base_count">number of base pairs</option> <option value="strain">strain from which sample was obtained</option> <option value="study_description">detailed sequencing study description</option> <option value="accession">accession number</option> <option value="assembly_level">assembly level</option> <option value="sample_accession">sample accession number</option> <option value="assembly_title">brief genome assembly description</option> <option value="study_title">brief sequencing study description</option> <option value="genome_representation">whether this is a full or partial genome</option> <option value="study_name">sequencing study name</option> <option value="study_accession">study accession number</option> </param> </when> <when value="fasta"/> </conditional> </when> <when value="sequence_release"> <repeat name="queries" title="Add a query"> <param name="combination_operation" type="select" label="Combination operation"> <option value="AND">AND</option> <option value="OR">OR</option> <option value="NOT">NOT</option> </param> <conditional name="filter_field"> <param name="field" type="select" label="Field to query"> <option value="mol_type">in vivo molecule type of the sequence</option> <option value="last_updated">date when last updated</option> <option value="sequence_md5"></option> <option value="haplotype">combination of alleles that are linked together on the same physical chromosome</option> <option value="serotype">serological variety of a species characterized by its antigenic properties</option> <option value="sex">sex of the organism from which the sample was obtained</option> <option value="keywords">keywords associated with sequence</option> <option value="collected_by">name of the person who collected the specimen</option> <option value="cell_line">cell line from which the sample was obtained</option> <option value="ecotype">a population within a given species displaying traits that reflect adaptation to a local habitat</option> <option value="bio_material">identifier for biological material including institute and collection code</option> <option value="identified_by">name of the taxonomist who identified the specimen</option> <option value="cell_type">cell type from which the sample was obtained</option> <option value="lab_host">scientific name of the laboratory host used to propagate the source organism for the sample</option> <option value="tax_division">taxonomic division</option> <option value="collection_date">date that the specimen was collected</option> <option value="specimen_voucher">identifier for the sample culture including institute and collection code</option> <option value="altitude">Altitude (m)</option> <option value="dev_stage">sample obtained from an organism in a specific developmental stage</option> <option value="isolate">individual isolate from which sample was obtained</option> <option value="location">geographic location of isolation of the sample</option> <option value="study_accession">study accession number</option> <option value="germline">the sample is an unrearranged molecule that was inherited from the parental germline</option> <option value="description">brief sequence description</option> <option value="accession">accession number</option> <option value="isolation_source">describes the physical, environmental and/or local geographical source of the sample</option> <option value="mating_type">mating type of the organism from which the sequence was obtained</option> <option value="tissue_type">tissue type from which the sample was obtained</option> <option value="sub_strain">name or identifier of a genetically or otherwise modified strain from which sample was obtained</option> <option value="tissue_lib">tissue library from which sample was obtained</option> <option value="cultivar">cultivar (cultivated variety) of plant from which sample was obtained</option> <option value="base_count">number of base pairs</option> <option value="topology">sequence topology: circular or linear</option> <option value="sub_species">name of sub-species of organism from which sample was obtained</option> <option value="environmental_sample">identifies sequences derived by direct molecular isolation from an environmental DNA sample</option> <option value="first_public">date when made public</option> <option value="strain">strain from which sample was obtained</option> <option value="country">locality of sample isolation: country names, oceans or seas, followed by regions and localities</option> <option value="variety">variety (varietas, a formal Linnaean rank) of organism from which sample was derived</option> <option value="host">natural (as opposed to laboratory) host to the organism from which sample was obtained</option> <option value="organelle">membrane-bound intracellular structure from which the sequence was obtained</option> <option value="serovar">serological variety of a species (usually a prokaryote) characterized by its antigenic properties</option> <option value="plasmid">name of naturally occurring plasmid from which the sequence was obtained</option> <option value="dataclass">sequence data class</option> <option value="culture_collection">identifier for the sample culture including institute and collection code</option> </param> <when value="mol_type"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/> </when> <when value="last_updated"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> <option value="lower">lower</option> <option value="equal or lower">equal or lower</option> <option value="higher">higher</option> <option value="equal or higher">equal or higher</option> </param> <param name="value" type="text" value="" label="A date in the format YYYY-MM-DD"/> </when> <when value="sequence_md5"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="haplotype"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="serotype"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="sex"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/> </when> <when value="keywords"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="collected_by"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="cell_line"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="ecotype"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="bio_material"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="identified_by"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="cell_type"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="lab_host"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="tax_division"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/> </when> <when value="collection_date"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> <option value="lower">lower</option> <option value="equal or lower">equal or lower</option> <option value="higher">higher</option> <option value="equal or higher">equal or higher</option> </param> <param name="value" type="text" value="" label="A date in the format YYYY-MM-DD"/> </when> <when value="specimen_voucher"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="altitude"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> <option value="lower">lower</option> <option value="equal or lower">equal or lower</option> <option value="higher">higher</option> <option value="equal or higher">equal or higher</option> </param> <param name="value" type="float" value="" label="Any integer"/> </when> <when value="dev_stage"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="isolate"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="location"> <conditional name="op"> <param name="operation" type="select" label="Operation"> <option value="geo_box2">All locations within a box defined by a centre point and a radius in km.</option> <option value="geo_box1">All locations within a box defined by the lower left (SW) and upper right (NE) points.</option> <option value="geo_circ">All locations within a circle defined by a centre point and a radius in km.</option> <option value="geo_lat">All locations within a latitude range given by a latitude and a radius in km.</option> <option value="geo_south">All locations south of a given latitude (inclusive).</option> <option value="geo_point">An exact lat/lon position</option> <option value="geo_north">All locations north of a given latitude (inclusive).</option> </param> <when value="geo_box2"> <param name="values" type="text" value="" label="latitude, longitude, radius (km)" help="Values separated by simple comma"/> </when> <when value="geo_box1"> <param name="values" type="text" value="" label="south-west latitude, south-west longitude, north-east latitude, north-east longitude" help="Values separated by simple comma"/> </when> <when value="geo_circ"> <param name="values" type="text" value="" label="latitude, longitude, radius (km)" help="Values separated by simple comma"/> </when> <when value="geo_lat"> <param name="values" type="text" value="" label="latitude, radius (km)" help="Values separated by simple comma"/> </when> <when value="geo_south"> <param name="values" type="text" value="" label="latitude" help="Values separated by simple comma"/> </when> <when value="geo_point"> <param name="values" type="text" value="" label="latitude, longitude" help="Values separated by simple comma"/> </when> <when value="geo_north"> <param name="values" type="text" value="" label="latitude" help="Values separated by simple comma"/> </when> </conditional> </when> <when value="study_accession"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="germline"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> </param> <param name="value" type="select" label="Value"> <option value="yes">yes</option> <option value="true">true</option> <option value="no">no</option> <option value="false">false</option> </param> </when> <when value="description"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="accession"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="isolation_source"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="mating_type"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="tissue_type"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="sub_strain"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="tissue_lib"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="cultivar"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="base_count"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> <option value="lower">lower</option> <option value="equal or lower">equal or lower</option> <option value="higher">higher</option> <option value="equal or higher">equal or higher</option> </param> <param name="value" type="float" value="" label="Any integer"/> </when> <when value="topology"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/> </when> <when value="sub_species"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="environmental_sample"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> </param> <param name="value" type="select" label="Value"> <option value="yes">yes</option> <option value="true">true</option> <option value="no">no</option> <option value="false">false</option> </param> </when> <when value="first_public"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> <option value="lower">lower</option> <option value="equal or lower">equal or lower</option> <option value="higher">higher</option> <option value="equal or higher">equal or higher</option> </param> <param name="value" type="text" value="" label="A date in the format YYYY-MM-DD"/> </when> <when value="strain"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="country"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="variety"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="host"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="organelle"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/> </when> <when value="serovar"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="plasmid"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="dataclass"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/> </when> <when value="culture_collection"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> </conditional> </repeat> <conditional name="display_opt"> <param argument="--display" type="select" label="Display option to specify the display format"> <expand macro="display_options"/> </param> <when value="xml"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> </when> <when value="text"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> </when> <when value="fastq"/> <when value="html"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> </when> <when value="report"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> <param argument="--fields" type="select" multiple="true" label="Fields to return"> <option value="accession">accession</option> <option value="base_count">base_count</option> <option value="bio_material">bio_material</option> <option value="cell_line">cell_line</option> <option value="cell_type">cell_type</option> <option value="collected_by">collected_by</option> <option value="collection_date">collection_date</option> <option value="country">country</option> <option value="cultivar">cultivar</option> <option value="culture_collection">culture_collection</option> <option value="dataclass">dataclass</option> <option value="description">description</option> <option value="dev_stage">dev_stage</option> <option value="ecotype">ecotype</option> <option value="environmental_sample">environmental_sample</option> <option value="first_public">first_public</option> <option value="germline">germline</option> <option value="host">host</option> <option value="identified_by">identified_by</option> <option value="isolate">isolate</option> <option value="isolation_source">isolation_source</option> <option value="keywords">keywords</option> <option value="lab_host">lab_host</option> <option value="last_updated">last_updated</option> <option value="location">location</option> <option value="mating_type">mating_type</option> <option value="mol_type">mol_type</option> <option value="organelle">organelle</option> <option value="serotype">serotype</option> <option value="serovar">serovar</option> <option value="sex">sex</option> <option value="submitted_sex">submitted_sex</option> <option value="specimen_voucher">specimen_voucher</option> <option value="strain">strain</option> <option value="sub_species">sub_species</option> <option value="sub_strain">sub_strain</option> <option value="tax_division">tax_division</option> <option value="tissue_lib">tissue_lib</option> <option value="tissue_type">tissue_type</option> <option value="topology">topology</option> <option value="variety">variety</option> <option value="tax_id">tax_id</option> <option value="scientific_name">scientific_name</option> <option value="altitude">altitude</option> <option value="haplotype">haplotype</option> <option value="plasmid">plasmid</option> <option value="study_accession">study_accession</option> <option value="sequence_md5">sequence_md5</option> </param> <param argument="--sortfields" type="select" optional="true" multiple="true" label="Fields to sort the results"> <option value="mol_type">in vivo molecule type of the sequence</option> <option value="last_updated">date when last updated</option> <option value="sequence_md5"></option> <option value="haplotype">combination of alleles that are linked together on the same physical chromosome</option> <option value="serotype">serological variety of a species characterized by its antigenic properties</option> <option value="sex">sex of the organism from which the sample was obtained</option> <option value="keywords">keywords associated with sequence</option> <option value="collected_by">name of the person who collected the specimen</option> <option value="cell_line">cell line from which the sample was obtained</option> <option value="ecotype">a population within a given species displaying traits that reflect adaptation to a local habitat</option> <option value="bio_material">identifier for biological material including institute and collection code</option> <option value="identified_by">name of the taxonomist who identified the specimen</option> <option value="cell_type">cell type from which the sample was obtained</option> <option value="lab_host">scientific name of the laboratory host used to propagate the source organism for the sample</option> <option value="tax_division">taxonomic division</option> <option value="collection_date">date that the specimen was collected</option> <option value="specimen_voucher">identifier for the sample culture including institute and collection code</option> <option value="altitude">Altitude (m)</option> <option value="dev_stage">sample obtained from an organism in a specific developmental stage</option> <option value="isolate">individual isolate from which sample was obtained</option> <option value="location">geographic location of isolation of the sample</option> <option value="study_accession">study accession number</option> <option value="germline">the sample is an unrearranged molecule that was inherited from the parental germline</option> <option value="description">brief sequence description</option> <option value="accession">accession number</option> <option value="isolation_source">describes the physical, environmental and/or local geographical source of the sample</option> <option value="mating_type">mating type of the organism from which the sequence was obtained</option> <option value="tissue_type">tissue type from which the sample was obtained</option> <option value="sub_strain">name or identifier of a genetically or otherwise modified strain from which sample was obtained</option> <option value="tissue_lib">tissue library from which sample was obtained</option> <option value="cultivar">cultivar (cultivated variety) of plant from which sample was obtained</option> <option value="base_count">number of base pairs</option> <option value="topology">sequence topology: circular or linear</option> <option value="sub_species">name of sub-species of organism from which sample was obtained</option> <option value="environmental_sample">identifies sequences derived by direct molecular isolation from an environmental DNA sample</option> <option value="first_public">date when made public</option> <option value="strain">strain from which sample was obtained</option> <option value="country">locality of sample isolation: country names, oceans or seas, followed by regions and localities</option> <option value="variety">variety (varietas, a formal Linnaean rank) of organism from which sample was derived</option> <option value="host">natural (as opposed to laboratory) host to the organism from which sample was obtained</option> <option value="organelle">membrane-bound intracellular structure from which the sequence was obtained</option> <option value="serovar">serological variety of a species (usually a prokaryote) characterized by its antigenic properties</option> <option value="plasmid">name of naturally occurring plasmid from which the sequence was obtained</option> <option value="dataclass">sequence data class</option> <option value="culture_collection">identifier for the sample culture including institute and collection code</option> </param> </when> <when value="fasta"/> </conditional> </when> <when value="wgs_set"> <repeat name="queries" title="Add a query"> <param name="combination_operation" type="select" label="Combination operation"> <option value="AND">AND</option> <option value="OR">OR</option> <option value="NOT">NOT</option> </param> <conditional name="filter_field"> <param name="field" type="select" label="Field to query"> <option value="mol_type">in vivo molecule type of the sequence</option> <option value="last_updated">date when last updated</option> <option value="lab_host">scientific name of the laboratory host used to propagate the source organism for the sample</option> <option value="haplotype">combination of alleles that are linked together on the same physical chromosome</option> <option value="accession">accession number</option> <option value="sex">sex of the organism from which the sample was obtained</option> <option value="cell_line">cell line from which the sample was obtained</option> <option value="host">natural (as opposed to laboratory) host to the organism from which sample was obtained</option> <option value="ecotype">a population within a given species displaying traits that reflect adaptation to a local habitat</option> <option value="bio_material">identifier for biological material including institute and collection code</option> <option value="identified_by">name of the taxonomist who identified the specimen</option> <option value="cell_type">cell type from which the sample was obtained</option> <option value="tax_division">taxonomic division</option> <option value="collection_date">date that the specimen was collected</option> <option value="specimen_voucher">identifier for the sample culture including institute and collection code</option> <option value="altitude">Altitude (m)</option> <option value="dev_stage">sample obtained from an organism in a specific developmental stage</option> <option value="isolate">individual isolate from which sample was obtained</option> <option value="location">geographic location of isolation of the sample</option> <option value="study_accession">study accession number</option> <option value="germline">the sample is an unrearranged molecule that was inherited from the parental germline</option> <option value="description">brief sequence description</option> <option value="tissue_lib">tissue library from which sample was obtained</option> <option value="isolation_source">describes the physical, environmental and/or local geographical source of the sample</option> <option value="mating_type">mating type of the organism from which the sequence was obtained</option> <option value="serovar">serological variety of a species (usually a prokaryote) characterized by its antigenic properties</option> <option value="serotype">serological variety of a species characterized by its antigenic properties</option> <option value="sub_strain">name or identifier of a genetically or otherwise modified strain from which sample was obtained</option> <option value="cultivar">cultivar (cultivated variety) of plant from which sample was obtained</option> <option value="collected_by">name of the person who collected the specimen</option> <option value="sub_species">name of sub-species of organism from which sample was obtained</option> <option value="first_public">date when made public</option> <option value="strain">strain from which sample was obtained</option> <option value="country">locality of sample isolation: country names, oceans or seas, followed by regions and localities</option> <option value="variety">variety (varietas, a formal Linnaean rank) of organism from which sample was derived</option> <option value="environmental_sample">identifies sequences derived by direct molecular isolation from an environmental DNA sample</option> <option value="tissue_type">tissue type from which the sample was obtained</option> <option value="keywords">keywords associated with sequence</option> <option value="culture_collection">identifier for the sample culture including institute and collection code</option> </param> <when value="mol_type"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/> </when> <when value="last_updated"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> <option value="lower">lower</option> <option value="equal or lower">equal or lower</option> <option value="higher">higher</option> <option value="equal or higher">equal or higher</option> </param> <param name="value" type="text" value="" label="A date in the format YYYY-MM-DD"/> </when> <when value="lab_host"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="haplotype"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="accession"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="sex"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/> </when> <when value="cell_line"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="host"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="ecotype"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="bio_material"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="identified_by"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="cell_type"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="tax_division"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/> </when> <when value="collection_date"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> <option value="lower">lower</option> <option value="equal or lower">equal or lower</option> <option value="higher">higher</option> <option value="equal or higher">equal or higher</option> </param> <param name="value" type="text" value="" label="A date in the format YYYY-MM-DD"/> </when> <when value="specimen_voucher"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="altitude"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> <option value="lower">lower</option> <option value="equal or lower">equal or lower</option> <option value="higher">higher</option> <option value="equal or higher">equal or higher</option> </param> <param name="value" type="float" value="" label="Any integer"/> </when> <when value="dev_stage"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="isolate"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="location"> <conditional name="op"> <param name="operation" type="select" label="Operation"> <option value="geo_box2">All locations within a box defined by a centre point and a radius in km.</option> <option value="geo_box1">All locations within a box defined by the lower left (SW) and upper right (NE) points.</option> <option value="geo_circ">All locations within a circle defined by a centre point and a radius in km.</option> <option value="geo_lat">All locations within a latitude range given by a latitude and a radius in km.</option> <option value="geo_south">All locations south of a given latitude (inclusive).</option> <option value="geo_point">An exact lat/lon position</option> <option value="geo_north">All locations north of a given latitude (inclusive).</option> </param> <when value="geo_box2"> <param name="values" type="text" value="" label="latitude, longitude, radius (km)" help="Values separated by simple comma"/> </when> <when value="geo_box1"> <param name="values" type="text" value="" label="south-west latitude, south-west longitude, north-east latitude, north-east longitude" help="Values separated by simple comma"/> </when> <when value="geo_circ"> <param name="values" type="text" value="" label="latitude, longitude, radius (km)" help="Values separated by simple comma"/> </when> <when value="geo_lat"> <param name="values" type="text" value="" label="latitude, radius (km)" help="Values separated by simple comma"/> </when> <when value="geo_south"> <param name="values" type="text" value="" label="latitude" help="Values separated by simple comma"/> </when> <when value="geo_point"> <param name="values" type="text" value="" label="latitude, longitude" help="Values separated by simple comma"/> </when> <when value="geo_north"> <param name="values" type="text" value="" label="latitude" help="Values separated by simple comma"/> </when> </conditional> </when> <when value="study_accession"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="germline"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> </param> <param name="value" type="select" label="Value"> <option value="yes">yes</option> <option value="true">true</option> <option value="no">no</option> <option value="false">false</option> </param> </when> <when value="description"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="tissue_lib"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="isolation_source"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="mating_type"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="serovar"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="serotype"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="sub_strain"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="cultivar"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="collected_by"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="sub_species"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="first_public"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> <option value="lower">lower</option> <option value="equal or lower">equal or lower</option> <option value="higher">higher</option> <option value="equal or higher">equal or higher</option> </param> <param name="value" type="text" value="" label="A date in the format YYYY-MM-DD"/> </when> <when value="strain"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="country"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="variety"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="environmental_sample"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> </param> <param name="value" type="select" label="Value"> <option value="yes">yes</option> <option value="true">true</option> <option value="no">no</option> <option value="false">false</option> </param> </when> <when value="tissue_type"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="keywords"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="culture_collection"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> </conditional> </repeat> <conditional name="display_opt"> <param argument="--display" type="select" label="Display option to specify the display format"> <expand macro="display_options"/> </param> <when value="xml"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> </when> <when value="text"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> </when> <when value="fastq"/> <when value="html"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> </when> <when value="report"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> <param argument="--fields" type="select" multiple="true" label="Fields to return"> <option value="accession">accession</option> <option value="bio_material">bio_material</option> <option value="cell_line">cell_line</option> <option value="cell_type">cell_type</option> <option value="collected_by">collected_by</option> <option value="collection_date">collection_date</option> <option value="country">country</option> <option value="cultivar">cultivar</option> <option value="culture_collection">culture_collection</option> <option value="description">description</option> <option value="dev_stage">dev_stage</option> <option value="ecotype">ecotype</option> <option value="environmental_sample">environmental_sample</option> <option value="first_public">first_public</option> <option value="germline">germline</option> <option value="host">host</option> <option value="identified_by">identified_by</option> <option value="isolate">isolate</option> <option value="isolation_source">isolation_source</option> <option value="keywords">keywords</option> <option value="lab_host">lab_host</option> <option value="last_updated">last_updated</option> <option value="location">location</option> <option value="mating_type">mating_type</option> <option value="mol_type">mol_type</option> <option value="serotype">serotype</option> <option value="serovar">serovar</option> <option value="sex">sex</option> <option value="submitted_sex">submitted_sex</option> <option value="specimen_voucher">specimen_voucher</option> <option value="strain">strain</option> <option value="sub_species">sub_species</option> <option value="sub_strain">sub_strain</option> <option value="tax_division">tax_division</option> <option value="tissue_lib">tissue_lib</option> <option value="tissue_type">tissue_type</option> <option value="variety">variety</option> <option value="tax_id">tax_id</option> <option value="scientific_name">scientific_name</option> <option value="altitude">altitude</option> <option value="haplotype">haplotype</option> <option value="study_accession">study_accession</option> <option value="set_files">set_files</option> </param> <param argument="--sortfields" type="select" optional="true" multiple="true" label="Fields to sort the results"> <option value="mol_type">in vivo molecule type of the sequence</option> <option value="last_updated">date when last updated</option> <option value="lab_host">scientific name of the laboratory host used to propagate the source organism for the sample</option> <option value="haplotype">combination of alleles that are linked together on the same physical chromosome</option> <option value="accession">accession number</option> <option value="sex">sex of the organism from which the sample was obtained</option> <option value="cell_line">cell line from which the sample was obtained</option> <option value="host">natural (as opposed to laboratory) host to the organism from which sample was obtained</option> <option value="ecotype">a population within a given species displaying traits that reflect adaptation to a local habitat</option> <option value="bio_material">identifier for biological material including institute and collection code</option> <option value="identified_by">name of the taxonomist who identified the specimen</option> <option value="cell_type">cell type from which the sample was obtained</option> <option value="tax_division">taxonomic division</option> <option value="collection_date">date that the specimen was collected</option> <option value="specimen_voucher">identifier for the sample culture including institute and collection code</option> <option value="altitude">Altitude (m)</option> <option value="dev_stage">sample obtained from an organism in a specific developmental stage</option> <option value="isolate">individual isolate from which sample was obtained</option> <option value="location">geographic location of isolation of the sample</option> <option value="study_accession">study accession number</option> <option value="germline">the sample is an unrearranged molecule that was inherited from the parental germline</option> <option value="description">brief sequence description</option> <option value="tissue_lib">tissue library from which sample was obtained</option> <option value="isolation_source">describes the physical, environmental and/or local geographical source of the sample</option> <option value="mating_type">mating type of the organism from which the sequence was obtained</option> <option value="serovar">serological variety of a species (usually a prokaryote) characterized by its antigenic properties</option> <option value="serotype">serological variety of a species characterized by its antigenic properties</option> <option value="sub_strain">name or identifier of a genetically or otherwise modified strain from which sample was obtained</option> <option value="cultivar">cultivar (cultivated variety) of plant from which sample was obtained</option> <option value="collected_by">name of the person who collected the specimen</option> <option value="sub_species">name of sub-species of organism from which sample was obtained</option> <option value="first_public">date when made public</option> <option value="strain">strain from which sample was obtained</option> <option value="country">locality of sample isolation: country names, oceans or seas, followed by regions and localities</option> <option value="variety">variety (varietas, a formal Linnaean rank) of organism from which sample was derived</option> <option value="environmental_sample">identifies sequences derived by direct molecular isolation from an environmental DNA sample</option> <option value="tissue_type">tissue type from which the sample was obtained</option> <option value="keywords">keywords associated with sequence</option> <option value="culture_collection">identifier for the sample culture including institute and collection code</option> </param> </when> <when value="fasta"/> </conditional> </when> <when value="study"> <repeat name="queries" title="Add a query"> <param name="combination_operation" type="select" label="Combination operation"> <option value="AND">AND</option> <option value="OR">OR</option> <option value="NOT">NOT</option> </param> <conditional name="filter_field"> <param name="field" type="select" label="Field to query"> <option value="broker_name">broker name</option> <option value="last_updated">date when last updated</option> <option value="center_name">Submitting center</option> <option value="study_description">detailed sequencing study description</option> <option value="breed">breed</option> <option value="isolate">individual isolate from which sample was obtained</option> <option value="study_name">sequencing study name</option> <option value="geo_accession">GEO accession</option> <option value="strain">strain from which sample was obtained</option> <option value="secondary_study_accession">project accession number</option> <option value="keywords">keywords associated with sequence</option> <option value="study_title">brief sequencing study description</option> <option value="cultivar">cultivar (cultivated variety) of plant from which sample was obtained</option> <option value="study_accession">study accession number</option> </param> <when value="broker_name"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/> </when> <when value="last_updated"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> <option value="lower">lower</option> <option value="equal or lower">equal or lower</option> <option value="higher">higher</option> <option value="equal or higher">equal or higher</option> </param> <param name="value" type="text" value="" label="A date in the format YYYY-MM-DD"/> </when> <when value="center_name"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="study_description"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="breed"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="isolate"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="study_name"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="geo_accession"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="strain"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="secondary_study_accession"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="keywords"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="study_title"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="cultivar"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="study_accession"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> </conditional> </repeat> <conditional name="display_opt"> <param argument="--display" type="select" label="Display option to specify the display format"> <expand macro="display_options"/> </param> <when value="xml"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> </when> <when value="text"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> </when> <when value="fastq"/> <when value="html"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> </when> <when value="report"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> <param argument="--fields" type="select" multiple="true" label="Fields to return"> <option value="study_accession">study_accession</option> <option value="secondary_study_accession">secondary_study_accession</option> <option value="study_description">study_description</option> <option value="study_name">study_name</option> <option value="study_title">study_title</option> <option value="tax_id">tax_id</option> <option value="scientific_name">scientific_name</option> <option value="strain">strain</option> <option value="breed">breed</option> <option value="cultivar">cultivar</option> <option value="isolate">isolate</option> <option value="center_name">center_name</option> <option value="broker_name">broker_name</option> <option value="keywords">keywords</option> <option value="geo_accession">geo_accession</option> <option value="last_updated">last_updated</option> </param> <param argument="--sortfields" type="select" optional="true" multiple="true" label="Fields to sort the results"> <option value="broker_name">broker name</option> <option value="last_updated">date when last updated</option> <option value="center_name">Submitting center</option> <option value="study_description">detailed sequencing study description</option> <option value="breed">breed</option> <option value="isolate">individual isolate from which sample was obtained</option> <option value="study_name">sequencing study name</option> <option value="geo_accession">GEO accession</option> <option value="strain">strain from which sample was obtained</option> <option value="secondary_study_accession">project accession number</option> <option value="keywords">keywords associated with sequence</option> <option value="study_title">brief sequencing study description</option> <option value="cultivar">cultivar (cultivated variety) of plant from which sample was obtained</option> <option value="study_accession">study accession number</option> </param> </when> <when value="fasta"/> </conditional> </when> <when value="taxon"> <repeat name="queries" title="Add a query"> <param name="combination_operation" type="select" label="Combination operation"> <option value="AND">AND</option> <option value="OR">OR</option> <option value="NOT">NOT</option> </param> <conditional name="filter_field"> <param name="field" type="select" label="Field to query"> </param> </conditional> </repeat> <conditional name="display_opt"> <param argument="--display" type="select" label="Display option to specify the display format"> <expand macro="display_options"/> </param> <when value="xml"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> </when> <when value="text"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> </when> <when value="fastq"/> <when value="html"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> </when> <when value="report"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> <param argument="--fields" type="select" multiple="true" label="Fields to return"> <option value="tax_id">tax_id</option> <option value="taxon_title">taxon_title</option> <option value="scientific_name">scientific_name</option> </param> <param argument="--sortfields" type="select" optional="true" multiple="true" label="Fields to sort the results"> </param> </when> <when value="fasta"/> </conditional> </when> <when value="coding_release"> <repeat name="queries" title="Add a query"> <param name="combination_operation" type="select" label="Combination operation"> <option value="AND">AND</option> <option value="OR">OR</option> <option value="NOT">NOT</option> </param> <conditional name="filter_field"> <param name="field" type="select" label="Field to query"> <option value="operon">name of the group of contiguous genes transcribed into a single transcript</option> <option value="mol_type">in vivo molecule type of the sequence</option> <option value="last_updated">date when last updated</option> <option value="lab_host">scientific name of the laboratory host used to propagate the source organism for the sample</option> <option value="transl_except">a single codon translation that does not conform to genetic code</option> <option value="haplotype">combination of alleles that are linked together on the same physical chromosome</option> <option value="serotype">serological variety of a species characterized by its antigenic properties</option> <option value="trans_splicing">indicates exons from two RNA molecules are ligated in intermolecular reaction to form mature RNA</option> <option value="sex">sex of the organism from which the sample was obtained</option> <option value="pseudo_gene">indicates that this feature is a pseudogene</option> <option value="standard_name">accepted standard name for a feature</option> <option value="collected_by">name of the person who collected the specimen</option> <option value="germline">the sample is an unrearranged molecule that was inherited from the parental germline</option> <option value="cell_type">cell type from which the sample was obtained</option> <option value="host">natural (as opposed to laboratory) host to the organism from which sample was obtained</option> <option value="inference">a structured description of non-experimental evidence</option> <option value="bio_material">identifier for biological material including institute and collection code</option> <option value="parent_accession">parent sequence accession number</option> <option value="identified_by">name of the taxonomist who identified the specimen</option> <option value="locus_tag">a submitter-supplied, systematic, stable identifier for a gene and its associated features</option> <option value="sequence_md5"></option> <option value="tax_division">taxonomic division</option> <option value="old_locus_tag">deprecated submitter-supplied, systematic, stable identifier for a gene and its associated features</option> <option value="specimen_voucher">identifier for the sample culture including institute and collection code</option> <option value="altitude">Altitude (m)</option> <option value="dev_stage">sample obtained from an organism in a specific developmental stage</option> <option value="isolate">individual isolate from which sample was obtained</option> <option value="ec_number">Enzyme Commission number for enzyme product of sequence</option> <option value="note">any comment or additional information</option> <option value="experiment">a brief description of the nature of the experimental evidence</option> <option value="location">geographic location of isolation of the sample</option> <option value="collection_date">date that the specimen was collected</option> <option value="allele">name of the allele for the given gene</option> <option value="protein_id">a stable protein identifier issued by INSDC</option> <option value="partial">differentiates between complete regions and partial ones (deprecated qualifier)</option> <option value="artificial_location">indicates location is modified to adjust for the presence of a frameshift or internal stop codon</option> <option value="function">function attributed to a sequence</option> <option value="map">genomic map position of feature</option> <option value="product">name of the product associated with the feature</option> <option value="description">brief sequence description</option> <option value="cell_line">cell line from which the sample was obtained</option> <option value="gene_synonym">synonymous, replaced, obsolete or former gene symbol</option> <option value="ecotype">a population within a given species displaying traits that reflect adaptation to a local habitat</option> <option value="exception">indicates that the coding region cannot be translated using standard biological rules</option> <option value="accession">accession number</option> <option value="isolation_source">describes the physical, environmental and/or local geographical source of the sample</option> <option value="mating_type">mating type of the organism from which the sequence was obtained</option> <option value="tissue_type">tissue type from which the sample was obtained</option> <option value="sub_strain">name or identifier of a genetically or otherwise modified strain from which sample was obtained</option> <option value="tissue_lib">tissue library from which sample was obtained</option> <option value="cultivar">cultivar (cultivated variety) of plant from which sample was obtained</option> <option value="base_count">number of base pairs</option> <option value="topology">sequence topology: circular or linear</option> <option value="sub_species">name of sub-species of organism from which sample was obtained</option> <option value="first_public">date when made public</option> <option value="strain">strain from which sample was obtained</option> <option value="country">locality of sample isolation: country names, oceans or seas, followed by regions and localities</option> <option value="variety">variety (varietas, a formal Linnaean rank) of organism from which sample was derived</option> <option value="pseudo">the feature is non-functional</option> <option value="environmental_sample">identifies sequences derived by direct molecular isolation from an environmental DNA sample</option> <option value="transl_table">indicates the genetic code table used if other than universal genetic code table</option> <option value="organelle">membrane-bound intracellular structure from which the sequence was obtained</option> <option value="ribosomal_slippage">indicates ribosomal slippage (change to an alternative reading frame) during protein translation</option> <option value="serovar">serological variety of a species (usually a prokaryote) characterized by its antigenic properties</option> <option value="keywords">keywords associated with sequence</option> <option value="dataclass">sequence data class</option> <option value="gene">symbol of the gene corresponding to a sequence region</option> <option value="codon_start">indicates the offset of the first complete codon relative to the first base of the coding feature</option> <option value="culture_collection">identifier for the sample culture including institute and collection code</option> </param> <when value="operon"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="mol_type"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/> </when> <when value="last_updated"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> <option value="lower">lower</option> <option value="equal or lower">equal or lower</option> <option value="higher">higher</option> <option value="equal or higher">equal or higher</option> </param> <param name="value" type="text" value="" label="A date in the format YYYY-MM-DD"/> </when> <when value="lab_host"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="transl_except"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="haplotype"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="serotype"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="trans_splicing"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> </param> <param name="value" type="select" label="Value"> <option value="yes">yes</option> <option value="true">true</option> <option value="no">no</option> <option value="false">false</option> </param> </when> <when value="sex"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/> </when> <when value="pseudo_gene"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/> </when> <when value="standard_name"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="collected_by"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="germline"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> </param> <param name="value" type="select" label="Value"> <option value="yes">yes</option> <option value="true">true</option> <option value="no">no</option> <option value="false">false</option> </param> </when> <when value="cell_type"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="host"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="inference"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="bio_material"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="parent_accession"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="identified_by"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="locus_tag"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="sequence_md5"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="tax_division"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/> </when> <when value="old_locus_tag"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="specimen_voucher"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="altitude"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> <option value="lower">lower</option> <option value="equal or lower">equal or lower</option> <option value="higher">higher</option> <option value="equal or higher">equal or higher</option> </param> <param name="value" type="float" value="" label="Any integer"/> </when> <when value="dev_stage"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="isolate"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="ec_number"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="note"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="experiment"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="location"> <conditional name="op"> <param name="operation" type="select" label="Operation"> <option value="geo_box2">All locations within a box defined by a centre point and a radius in km.</option> <option value="geo_box1">All locations within a box defined by the lower left (SW) and upper right (NE) points.</option> <option value="geo_circ">All locations within a circle defined by a centre point and a radius in km.</option> <option value="geo_lat">All locations within a latitude range given by a latitude and a radius in km.</option> <option value="geo_south">All locations south of a given latitude (inclusive).</option> <option value="geo_point">An exact lat/lon position</option> <option value="geo_north">All locations north of a given latitude (inclusive).</option> </param> <when value="geo_box2"> <param name="values" type="text" value="" label="latitude, longitude, radius (km)" help="Values separated by simple comma"/> </when> <when value="geo_box1"> <param name="values" type="text" value="" label="south-west latitude, south-west longitude, north-east latitude, north-east longitude" help="Values separated by simple comma"/> </when> <when value="geo_circ"> <param name="values" type="text" value="" label="latitude, longitude, radius (km)" help="Values separated by simple comma"/> </when> <when value="geo_lat"> <param name="values" type="text" value="" label="latitude, radius (km)" help="Values separated by simple comma"/> </when> <when value="geo_south"> <param name="values" type="text" value="" label="latitude" help="Values separated by simple comma"/> </when> <when value="geo_point"> <param name="values" type="text" value="" label="latitude, longitude" help="Values separated by simple comma"/> </when> <when value="geo_north"> <param name="values" type="text" value="" label="latitude" help="Values separated by simple comma"/> </when> </conditional> </when> <when value="collection_date"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> <option value="lower">lower</option> <option value="equal or lower">equal or lower</option> <option value="higher">higher</option> <option value="equal or higher">equal or higher</option> </param> <param name="value" type="text" value="" label="A date in the format YYYY-MM-DD"/> </when> <when value="allele"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="protein_id"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="partial"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> </param> <param name="value" type="select" label="Value"> <option value="yes">yes</option> <option value="true">true</option> <option value="no">no</option> <option value="false">false</option> </param> </when> <when value="artificial_location"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/> </when> <when value="function"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="map"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="product"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="description"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="cell_line"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="gene_synonym"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="ecotype"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="exception"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="accession"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="isolation_source"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="mating_type"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="tissue_type"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="sub_strain"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="tissue_lib"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="cultivar"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="base_count"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> <option value="lower">lower</option> <option value="equal or lower">equal or lower</option> <option value="higher">higher</option> <option value="equal or higher">equal or higher</option> </param> <param name="value" type="float" value="" label="Any integer"/> </when> <when value="topology"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/> </when> <when value="sub_species"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="first_public"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> <option value="lower">lower</option> <option value="equal or lower">equal or lower</option> <option value="higher">higher</option> <option value="equal or higher">equal or higher</option> </param> <param name="value" type="text" value="" label="A date in the format YYYY-MM-DD"/> </when> <when value="strain"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="country"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="variety"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="pseudo"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> </param> <param name="value" type="select" label="Value"> <option value="yes">yes</option> <option value="true">true</option> <option value="no">no</option> <option value="false">false</option> </param> </when> <when value="environmental_sample"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> </param> <param name="value" type="select" label="Value"> <option value="yes">yes</option> <option value="true">true</option> <option value="no">no</option> <option value="false">false</option> </param> </when> <when value="transl_table"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/> </when> <when value="organelle"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/> </when> <when value="ribosomal_slippage"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> </param> <param name="value" type="select" label="Value"> <option value="yes">yes</option> <option value="true">true</option> <option value="no">no</option> <option value="false">false</option> </param> </when> <when value="serovar"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="keywords"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="dataclass"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/> </when> <when value="gene"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="codon_start"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/> </when> <when value="culture_collection"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> </conditional> </repeat> <conditional name="display_opt"> <param argument="--display" type="select" label="Display option to specify the display format"> <expand macro="display_options"/> </param> <when value="xml"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> </when> <when value="text"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> </when> <when value="fastq"/> <when value="html"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> </when> <when value="report"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> <param argument="--fields" type="select" multiple="true" label="Fields to return"> <option value="accession">accession</option> <option value="base_count">base_count</option> <option value="bio_material">bio_material</option> <option value="cell_line">cell_line</option> <option value="cell_type">cell_type</option> <option value="collected_by">collected_by</option> <option value="collection_date">collection_date</option> <option value="country">country</option> <option value="cultivar">cultivar</option> <option value="culture_collection">culture_collection</option> <option value="dataclass">dataclass</option> <option value="description">description</option> <option value="dev_stage">dev_stage</option> <option value="ecotype">ecotype</option> <option value="environmental_sample">environmental_sample</option> <option value="first_public">first_public</option> <option value="germline">germline</option> <option value="host">host</option> <option value="identified_by">identified_by</option> <option value="isolate">isolate</option> <option value="isolation_source">isolation_source</option> <option value="keywords">keywords</option> <option value="lab_host">lab_host</option> <option value="last_updated">last_updated</option> <option value="location">location</option> <option value="mating_type">mating_type</option> <option value="mol_type">mol_type</option> <option value="organelle">organelle</option> <option value="serotype">serotype</option> <option value="serovar">serovar</option> <option value="sex">sex</option> <option value="submitted_sex">submitted_sex</option> <option value="specimen_voucher">specimen_voucher</option> <option value="strain">strain</option> <option value="sub_species">sub_species</option> <option value="sub_strain">sub_strain</option> <option value="tax_division">tax_division</option> <option value="tissue_lib">tissue_lib</option> <option value="tissue_type">tissue_type</option> <option value="variety">variety</option> <option value="allele">allele</option> <option value="artificial_location">artificial_location</option> <option value="codon_start">codon_start</option> <option value="ec_number">ec_number</option> <option value="exception">exception</option> <option value="experiment">experiment</option> <option value="function">function</option> <option value="topology">topology</option> <option value="gene">gene</option> <option value="gene_synonym">gene_synonym</option> <option value="inference">inference</option> <option value="locus_tag">locus_tag</option> <option value="map">map</option> <option value="note">note</option> <option value="old_locus_tag">old_locus_tag</option> <option value="operon">operon</option> <option value="partial">partial</option> <option value="product">product</option> <option value="protein_id">protein_id</option> <option value="pseudo">pseudo</option> <option value="pseudo_gene">pseudo_gene</option> <option value="ribosomal_slippage">ribosomal_slippage</option> <option value="standard_name">standard_name</option> <option value="trans_splicing">trans_splicing</option> <option value="transl_except">transl_except</option> <option value="transl_table">transl_table</option> <option value="tax_id">tax_id</option> <option value="scientific_name">scientific_name</option> <option value="parent_accession">parent_accession</option> <option value="altitude">altitude</option> <option value="haplotype">haplotype</option> <option value="sequence_md5">sequence_md5</option> </param> <param argument="--sortfields" type="select" optional="true" multiple="true" label="Fields to sort the results"> <option value="operon">name of the group of contiguous genes transcribed into a single transcript</option> <option value="mol_type">in vivo molecule type of the sequence</option> <option value="last_updated">date when last updated</option> <option value="lab_host">scientific name of the laboratory host used to propagate the source organism for the sample</option> <option value="transl_except">a single codon translation that does not conform to genetic code</option> <option value="haplotype">combination of alleles that are linked together on the same physical chromosome</option> <option value="serotype">serological variety of a species characterized by its antigenic properties</option> <option value="trans_splicing">indicates exons from two RNA molecules are ligated in intermolecular reaction to form mature RNA</option> <option value="sex">sex of the organism from which the sample was obtained</option> <option value="pseudo_gene">indicates that this feature is a pseudogene</option> <option value="standard_name">accepted standard name for a feature</option> <option value="collected_by">name of the person who collected the specimen</option> <option value="germline">the sample is an unrearranged molecule that was inherited from the parental germline</option> <option value="cell_type">cell type from which the sample was obtained</option> <option value="host">natural (as opposed to laboratory) host to the organism from which sample was obtained</option> <option value="inference">a structured description of non-experimental evidence</option> <option value="bio_material">identifier for biological material including institute and collection code</option> <option value="parent_accession">parent sequence accession number</option> <option value="identified_by">name of the taxonomist who identified the specimen</option> <option value="locus_tag">a submitter-supplied, systematic, stable identifier for a gene and its associated features</option> <option value="sequence_md5"></option> <option value="tax_division">taxonomic division</option> <option value="old_locus_tag">deprecated submitter-supplied, systematic, stable identifier for a gene and its associated features</option> <option value="specimen_voucher">identifier for the sample culture including institute and collection code</option> <option value="altitude">Altitude (m)</option> <option value="dev_stage">sample obtained from an organism in a specific developmental stage</option> <option value="isolate">individual isolate from which sample was obtained</option> <option value="ec_number">Enzyme Commission number for enzyme product of sequence</option> <option value="note">any comment or additional information</option> <option value="experiment">a brief description of the nature of the experimental evidence</option> <option value="location">geographic location of isolation of the sample</option> <option value="collection_date">date that the specimen was collected</option> <option value="allele">name of the allele for the given gene</option> <option value="protein_id">a stable protein identifier issued by INSDC</option> <option value="partial">differentiates between complete regions and partial ones (deprecated qualifier)</option> <option value="artificial_location">indicates location is modified to adjust for the presence of a frameshift or internal stop codon</option> <option value="function">function attributed to a sequence</option> <option value="map">genomic map position of feature</option> <option value="product">name of the product associated with the feature</option> <option value="description">brief sequence description</option> <option value="cell_line">cell line from which the sample was obtained</option> <option value="gene_synonym">synonymous, replaced, obsolete or former gene symbol</option> <option value="ecotype">a population within a given species displaying traits that reflect adaptation to a local habitat</option> <option value="exception">indicates that the coding region cannot be translated using standard biological rules</option> <option value="accession">accession number</option> <option value="isolation_source">describes the physical, environmental and/or local geographical source of the sample</option> <option value="mating_type">mating type of the organism from which the sequence was obtained</option> <option value="tissue_type">tissue type from which the sample was obtained</option> <option value="sub_strain">name or identifier of a genetically or otherwise modified strain from which sample was obtained</option> <option value="tissue_lib">tissue library from which sample was obtained</option> <option value="cultivar">cultivar (cultivated variety) of plant from which sample was obtained</option> <option value="base_count">number of base pairs</option> <option value="topology">sequence topology: circular or linear</option> <option value="sub_species">name of sub-species of organism from which sample was obtained</option> <option value="first_public">date when made public</option> <option value="strain">strain from which sample was obtained</option> <option value="country">locality of sample isolation: country names, oceans or seas, followed by regions and localities</option> <option value="variety">variety (varietas, a formal Linnaean rank) of organism from which sample was derived</option> <option value="pseudo">the feature is non-functional</option> <option value="environmental_sample">identifies sequences derived by direct molecular isolation from an environmental DNA sample</option> <option value="transl_table">indicates the genetic code table used if other than universal genetic code table</option> <option value="organelle">membrane-bound intracellular structure from which the sequence was obtained</option> <option value="ribosomal_slippage">indicates ribosomal slippage (change to an alternative reading frame) during protein translation</option> <option value="serovar">serological variety of a species (usually a prokaryote) characterized by its antigenic properties</option> <option value="keywords">keywords associated with sequence</option> <option value="dataclass">sequence data class</option> <option value="gene">symbol of the gene corresponding to a sequence region</option> <option value="codon_start">indicates the offset of the first complete codon relative to the first base of the coding feature</option> <option value="culture_collection">identifier for the sample culture including institute and collection code</option> </param> </when> <when value="fasta"/> </conditional> </when> <when value="sample"> <repeat name="queries" title="Add a query"> <param name="combination_operation" type="select" label="Combination operation"> <option value="AND">AND</option> <option value="OR">OR</option> <option value="NOT">NOT</option> </param> <conditional name="filter_field"> <param name="field" type="select" label="Field to query"> <option value="secondary_sample_accession">secondary sample accession number</option> <option value="environment_material">Environment (Material)</option> <option value="host_sex">physical sex of the host</option> <option value="ecotype">a population within a given species displaying traits that reflect adaptation to a local habitat</option> <option value="center_name">Submitting center</option> <option value="serotype">serological variety of a species characterized by its antigenic properties</option> <option value="sex">sex of the organism from which the sample was obtained</option> <option value="host_phenotype">phenotype of host</option> <option value="sampling_site">the site/station where this sample was collection</option> <option value="sequencing_method">sequencing method used</option> <option value="cell_line">cell line from which the sample was obtained</option> <option value="bio_material">identifier for biological material including institute and collection code</option> <option value="target_gene">targeted gene or locus name for marker gene studies</option> <option value="experimental_factor">variable aspects of the experimental design</option> <option value="identified_by">name of the taxonomist who identified the specimen</option> <option value="cell_type">cell type from which the sample was obtained</option> <option value="temperature">Temperature (C)</option> <option value="sampling_platform">the large infrastructure from which this sample was collected</option> <option value="variety">variety (varietas, a formal Linnaean rank) of organism from which sample was derived</option> <option value="collection_date">date that the specimen was collected</option> <option value="specimen_voucher">identifier for the sample culture including institute and collection code</option> <option value="altitude">Altitude (m)</option> <option value="dev_stage">sample obtained from an organism in a specific developmental stage</option> <option value="isolate">individual isolate from which sample was obtained</option> <option value="investigation_type">the study type targeted by the sequencing</option> <option value="serovar">serological variety of a species (usually a prokaryote) characterized by its antigenic properties</option> <option value="protocol_label">the protocol used to produce the sample</option> <option value="location">geographic location of isolation of the sample</option> <option value="host_genotype">genotype of host</option> <option value="ph">pH</option> <option value="broker_name">broker name</option> <option value="germline">the sample is an unrearranged molecule that was inherited from the parental germline</option> <option value="project_name">name of the project within which the sequencing was organized</option> <option value="elevation">Elevation (m)</option> <option value="description">brief sequence description</option> <option value="sample_alias">submitter's name for the sample</option> <option value="checklist">checklist name (or ID)</option> <option value="sampling_campaign">the activity within which this sample was collected</option> <option value="accession">accession number</option> <option value="isolation_source">describes the physical, environmental and/or local geographical source of the sample</option> <option value="mating_type">mating type of the organism from which the sequence was obtained</option> <option value="tissue_type">tissue type from which the sample was obtained</option> <option value="sub_strain">name or identifier of a genetically or otherwise modified strain from which sample was obtained</option> <option value="tissue_lib">tissue library from which sample was obtained</option> <option value="cultivar">cultivar (cultivated variety) of plant from which sample was obtained</option> <option value="environment_biome">Environment (Biome)</option> <option value="environmental_package">MIGS/MIMS/MIMARKS extension for reporting (from environment where the sample was obtained)</option> <option value="sub_species">name of sub-species of organism from which sample was obtained</option> <option value="first_public">date when made public</option> <option value="environment_feature">Environment (Feature)</option> <option value="host">natural (as opposed to laboratory) host to the organism from which sample was obtained</option> <option value="country">locality of sample isolation: country names, oceans or seas, followed by regions and localities</option> <option value="collected_by">name of the person who collected the specimen</option> <option value="environmental_sample">identifies sequences derived by direct molecular isolation from an environmental DNA sample</option> <option value="salinity">Salinity (PSU)</option> <option value="host_status">condition of host (eg. diseased or healthy)</option> <option value="strain">strain from which sample was obtained</option> <option value="depth">Depth (m)</option> <option value="host_tax_id">NCBI taxon id of the host</option> <option value="host_body_site">name of body site from where the sample was obtained</option> <option value="host_growth_conditions">literature reference giving growth conditions of the host</option> <option value="sample_collection">the method or deviced employed for collecting the sample</option> <option value="culture_collection">identifier for the sample culture including institute and collection code</option> </param> <when value="secondary_sample_accession"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="environment_material"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="host_sex"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/> </when> <when value="ecotype"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="center_name"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="serotype"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="sex"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/> </when> <when value="host_phenotype"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="sampling_site"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="sequencing_method"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="cell_line"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="bio_material"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="target_gene"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="experimental_factor"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="identified_by"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="cell_type"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="temperature"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> <option value="lower">lower</option> <option value="equal or lower">equal or lower</option> <option value="higher">higher</option> <option value="equal or higher">equal or higher</option> </param> <param name="value" type="float" value="" label="Any integer"/> </when> <when value="sampling_platform"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="variety"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="collection_date"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> <option value="lower">lower</option> <option value="equal or lower">equal or lower</option> <option value="higher">higher</option> <option value="equal or higher">equal or higher</option> </param> <param name="value" type="text" value="" label="A date in the format YYYY-MM-DD"/> </when> <when value="specimen_voucher"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="altitude"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> <option value="lower">lower</option> <option value="equal or lower">equal or lower</option> <option value="higher">higher</option> <option value="equal or higher">equal or higher</option> </param> <param name="value" type="float" value="" label="Any integer"/> </when> <when value="dev_stage"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="isolate"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="investigation_type"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/> </when> <when value="serovar"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="protocol_label"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="location"> <conditional name="op"> <param name="operation" type="select" label="Operation"> <option value="geo_box2">All locations within a box defined by a centre point and a radius in km.</option> <option value="geo_box1">All locations within a box defined by the lower left (SW) and upper right (NE) points.</option> <option value="geo_circ">All locations within a circle defined by a centre point and a radius in km.</option> <option value="geo_lat">All locations within a latitude range given by a latitude and a radius in km.</option> <option value="geo_south">All locations south of a given latitude (inclusive).</option> <option value="geo_point">An exact lat/lon position</option> <option value="geo_north">All locations north of a given latitude (inclusive).</option> </param> <when value="geo_box2"> <param name="values" type="text" value="" label="latitude, longitude, radius (km)" help="Values separated by simple comma"/> </when> <when value="geo_box1"> <param name="values" type="text" value="" label="south-west latitude, south-west longitude, north-east latitude, north-east longitude" help="Values separated by simple comma"/> </when> <when value="geo_circ"> <param name="values" type="text" value="" label="latitude, longitude, radius (km)" help="Values separated by simple comma"/> </when> <when value="geo_lat"> <param name="values" type="text" value="" label="latitude, radius (km)" help="Values separated by simple comma"/> </when> <when value="geo_south"> <param name="values" type="text" value="" label="latitude" help="Values separated by simple comma"/> </when> <when value="geo_point"> <param name="values" type="text" value="" label="latitude, longitude" help="Values separated by simple comma"/> </when> <when value="geo_north"> <param name="values" type="text" value="" label="latitude" help="Values separated by simple comma"/> </when> </conditional> </when> <when value="host_genotype"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="ph"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> <option value="lower">lower</option> <option value="equal or lower">equal or lower</option> <option value="higher">higher</option> <option value="equal or higher">equal or higher</option> </param> <param name="value" type="float" value="" label="Any integer"/> </when> <when value="broker_name"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/> </when> <when value="germline"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> </param> <param name="value" type="select" label="Value"> <option value="yes">yes</option> <option value="true">true</option> <option value="no">no</option> <option value="false">false</option> </param> </when> <when value="project_name"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="elevation"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> <option value="lower">lower</option> <option value="equal or lower">equal or lower</option> <option value="higher">higher</option> <option value="equal or higher">equal or higher</option> </param> <param name="value" type="float" value="" label="Any integer"/> </when> <when value="description"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="sample_alias"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="checklist"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/> </when> <when value="sampling_campaign"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="accession"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="isolation_source"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="mating_type"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="tissue_type"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="sub_strain"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="tissue_lib"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="cultivar"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="environment_biome"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="environmental_package"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/> </when> <when value="sub_species"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="first_public"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> <option value="lower">lower</option> <option value="equal or lower">equal or lower</option> <option value="higher">higher</option> <option value="equal or higher">equal or higher</option> </param> <param name="value" type="text" value="" label="A date in the format YYYY-MM-DD"/> </when> <when value="environment_feature"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="host"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="country"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="collected_by"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="environmental_sample"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> </param> <param name="value" type="select" label="Value"> <option value="yes">yes</option> <option value="true">true</option> <option value="no">no</option> <option value="false">false</option> </param> </when> <when value="salinity"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> <option value="lower">lower</option> <option value="equal or lower">equal or lower</option> <option value="higher">higher</option> <option value="equal or higher">equal or higher</option> </param> <param name="value" type="float" value="" label="Any integer"/> </when> <when value="host_status"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="strain"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="depth"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> <option value="lower">lower</option> <option value="equal or lower">equal or lower</option> <option value="higher">higher</option> <option value="equal or higher">equal or higher</option> </param> <param name="value" type="float" value="" label="Any integer"/> </when> <when value="host_tax_id"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> <option value="lower">lower</option> <option value="equal or lower">equal or lower</option> <option value="higher">higher</option> <option value="equal or higher">equal or higher</option> </param> <param name="value" type="float" value="" label="Any integer"/> </when> <when value="host_body_site"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="host_growth_conditions"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="sample_collection"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="culture_collection"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> </conditional> </repeat> <conditional name="display_opt"> <param argument="--display" type="select" label="Display option to specify the display format"> <expand macro="display_options"/> </param> <when value="xml"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> </when> <when value="text"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> </when> <when value="fastq"/> <when value="html"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> </when> <when value="report"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> <param argument="--fields" type="select" multiple="true" label="Fields to return"> <option value="accession">accession</option> <option value="secondary_sample_accession">secondary_sample_accession</option> <option value="bio_material">bio_material</option> <option value="cell_line">cell_line</option> <option value="cell_type">cell_type</option> <option value="collected_by">collected_by</option> <option value="collection_date">collection_date</option> <option value="country">country</option> <option value="cultivar">cultivar</option> <option value="culture_collection">culture_collection</option> <option value="description">description</option> <option value="dev_stage">dev_stage</option> <option value="ecotype">ecotype</option> <option value="environmental_sample">environmental_sample</option> <option value="first_public">first_public</option> <option value="germline">germline</option> <option value="identified_by">identified_by</option> <option value="isolate">isolate</option> <option value="isolation_source">isolation_source</option> <option value="location">location</option> <option value="mating_type">mating_type</option> <option value="serotype">serotype</option> <option value="serovar">serovar</option> <option value="sex">sex</option> <option value="submitted_sex">submitted_sex</option> <option value="specimen_voucher">specimen_voucher</option> <option value="strain">strain</option> <option value="sub_species">sub_species</option> <option value="sub_strain">sub_strain</option> <option value="tissue_lib">tissue_lib</option> <option value="tissue_type">tissue_type</option> <option value="variety">variety</option> <option value="tax_id">tax_id</option> <option value="scientific_name">scientific_name</option> <option value="sample_alias">sample_alias</option> <option value="checklist">checklist</option> <option value="center_name">center_name</option> <option value="depth">depth</option> <option value="elevation">elevation</option> <option value="altitude">altitude</option> <option value="environment_biome">environment_biome</option> <option value="environment_feature">environment_feature</option> <option value="environment_material">environment_material</option> <option value="temperature">temperature</option> <option value="salinity">salinity</option> <option value="sampling_campaign">sampling_campaign</option> <option value="sampling_site">sampling_site</option> <option value="sampling_platform">sampling_platform</option> <option value="protocol_label">protocol_label</option> <option value="project_name">project_name</option> <option value="host">host</option> <option value="host_tax_id">host_tax_id</option> <option value="host_status">host_status</option> <option value="host_sex">host_sex</option> <option value="submitted_host_sex">submitted_host_sex</option> <option value="host_body_site">host_body_site</option> <option value="host_gravidity">host_gravidity</option> <option value="host_phenotype">host_phenotype</option> <option value="host_genotype">host_genotype</option> <option value="host_growth_conditions">host_growth_conditions</option> <option value="environmental_package">environmental_package</option> <option value="investigation_type">investigation_type</option> <option value="experimental_factor">experimental_factor</option> <option value="sample_collection">sample_collection</option> <option value="sequencing_method">sequencing_method</option> <option value="target_gene">target_gene</option> <option value="ph">ph</option> <option value="broker_name">broker_name</option> </param> <param argument="--sortfields" type="select" optional="true" multiple="true" label="Fields to sort the results"> <option value="secondary_sample_accession">secondary sample accession number</option> <option value="environment_material">Environment (Material)</option> <option value="host_sex">physical sex of the host</option> <option value="ecotype">a population within a given species displaying traits that reflect adaptation to a local habitat</option> <option value="center_name">Submitting center</option> <option value="serotype">serological variety of a species characterized by its antigenic properties</option> <option value="sex">sex of the organism from which the sample was obtained</option> <option value="host_phenotype">phenotype of host</option> <option value="sampling_site">the site/station where this sample was collection</option> <option value="sequencing_method">sequencing method used</option> <option value="cell_line">cell line from which the sample was obtained</option> <option value="bio_material">identifier for biological material including institute and collection code</option> <option value="target_gene">targeted gene or locus name for marker gene studies</option> <option value="experimental_factor">variable aspects of the experimental design</option> <option value="identified_by">name of the taxonomist who identified the specimen</option> <option value="cell_type">cell type from which the sample was obtained</option> <option value="temperature">Temperature (C)</option> <option value="sampling_platform">the large infrastructure from which this sample was collected</option> <option value="variety">variety (varietas, a formal Linnaean rank) of organism from which sample was derived</option> <option value="collection_date">date that the specimen was collected</option> <option value="specimen_voucher">identifier for the sample culture including institute and collection code</option> <option value="altitude">Altitude (m)</option> <option value="dev_stage">sample obtained from an organism in a specific developmental stage</option> <option value="isolate">individual isolate from which sample was obtained</option> <option value="investigation_type">the study type targeted by the sequencing</option> <option value="serovar">serological variety of a species (usually a prokaryote) characterized by its antigenic properties</option> <option value="protocol_label">the protocol used to produce the sample</option> <option value="location">geographic location of isolation of the sample</option> <option value="host_genotype">genotype of host</option> <option value="ph">pH</option> <option value="broker_name">broker name</option> <option value="germline">the sample is an unrearranged molecule that was inherited from the parental germline</option> <option value="project_name">name of the project within which the sequencing was organized</option> <option value="elevation">Elevation (m)</option> <option value="description">brief sequence description</option> <option value="sample_alias">submitter's name for the sample</option> <option value="checklist">checklist name (or ID)</option> <option value="sampling_campaign">the activity within which this sample was collected</option> <option value="accession">accession number</option> <option value="isolation_source">describes the physical, environmental and/or local geographical source of the sample</option> <option value="mating_type">mating type of the organism from which the sequence was obtained</option> <option value="tissue_type">tissue type from which the sample was obtained</option> <option value="sub_strain">name or identifier of a genetically or otherwise modified strain from which sample was obtained</option> <option value="tissue_lib">tissue library from which sample was obtained</option> <option value="cultivar">cultivar (cultivated variety) of plant from which sample was obtained</option> <option value="environment_biome">Environment (Biome)</option> <option value="environmental_package">MIGS/MIMS/MIMARKS extension for reporting (from environment where the sample was obtained)</option> <option value="sub_species">name of sub-species of organism from which sample was obtained</option> <option value="first_public">date when made public</option> <option value="environment_feature">Environment (Feature)</option> <option value="host">natural (as opposed to laboratory) host to the organism from which sample was obtained</option> <option value="country">locality of sample isolation: country names, oceans or seas, followed by regions and localities</option> <option value="collected_by">name of the person who collected the specimen</option> <option value="environmental_sample">identifies sequences derived by direct molecular isolation from an environmental DNA sample</option> <option value="salinity">Salinity (PSU)</option> <option value="host_status">condition of host (eg. diseased or healthy)</option> <option value="strain">strain from which sample was obtained</option> <option value="depth">Depth (m)</option> <option value="host_tax_id">NCBI taxon id of the host</option> <option value="host_body_site">name of body site from where the sample was obtained</option> <option value="host_growth_conditions">literature reference giving growth conditions of the host</option> <option value="sample_collection">the method or deviced employed for collecting the sample</option> <option value="culture_collection">identifier for the sample culture including institute and collection code</option> </param> </when> <when value="fasta"/> </conditional> </when> <when value="environmental"> <repeat name="queries" title="Add a query"> <param name="combination_operation" type="select" label="Combination operation"> <option value="AND">AND</option> <option value="OR">OR</option> <option value="NOT">NOT</option> </param> <conditional name="filter_field"> <param name="field" type="select" label="Field to query"> <option value="secondary_sample_accession">secondary sample accession number</option> <option value="environment_material">Environment (Material)</option> <option value="dev_stage">sample obtained from an organism in a specific developmental stage</option> <option value="event_label">label given to sampling event</option> <option value="center_name">Submitting center</option> <option value="accession">accession number</option> <option value="host_phenotype">phenotype of host</option> <option value="cell_line">cell line from which the sample was obtained</option> <option value="bio_material">identifier for biological material including institute and collection code</option> <option value="target_gene">targeted gene or locus name for marker gene studies</option> <option value="experimental_factor">variable aspects of the experimental design</option> <option value="identified_by">name of the taxonomist who identified the specimen</option> <option value="temperature">Temperature (C)</option> <option value="sampling_platform">the large infrastructure from which this sample was collected</option> <option value="collected_by">name of the person who collected the specimen</option> <option value="collection_date">date that the specimen was collected</option> <option value="altitude">Altitude (m)</option> <option value="host_sex">physical sex of the host</option> <option value="investigation_type">the study type targeted by the sequencing</option> <option value="location">geographic location of isolation of the sample</option> <option value="host_genotype">genotype of host</option> <option value="ph">pH</option> <option value="broker_name">broker name</option> <option value="project_name">name of the project within which the sequencing was organized</option> <option value="elevation">Elevation (m)</option> <option value="description">brief sequence description</option> <option value="sample_alias">submitter's name for the sample</option> <option value="checklist">checklist name (or ID)</option> <option value="sampling_campaign">the activity within which this sample was collected</option> <option value="protocol_label">the protocol used to produce the sample</option> <option value="isolation_source">describes the physical, environmental and/or local geographical source of the sample</option> <option value="sampling_site">the site/station where this sample was collection</option> <option value="host_tax_id">NCBI taxon id of the host</option> <option value="cultivar">cultivar (cultivated variety) of plant from which sample was obtained</option> <option value="environment_biome">Environment (Biome)</option> <option value="environmental_package">MIGS/MIMS/MIMARKS extension for reporting (from environment where the sample was obtained)</option> <option value="marine_region">geographical origin of the sample as defined by the marine region</option> <option value="first_public">date when made public</option> <option value="environment_feature">Environment (Feature)</option> <option value="country">locality of sample isolation: country names, oceans or seas, followed by regions and localities</option> <option value="host">natural (as opposed to laboratory) host to the organism from which sample was obtained</option> <option value="salinity">Salinity (PSU)</option> <option value="host_status">condition of host (eg. diseased or healthy)</option> <option value="strain">strain from which sample was obtained</option> <option value="depth">Depth (m)</option> <option value="tissue_type">tissue type from which the sample was obtained</option> <option value="host_body_site">name of body site from where the sample was obtained</option> <option value="host_growth_conditions">literature reference giving growth conditions of the host</option> <option value="sample_collection">the method or deviced employed for collecting the sample</option> <option value="sequencing_method">sequencing method used</option> </param> <when value="secondary_sample_accession"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="environment_material"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="dev_stage"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="event_label"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="center_name"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="accession"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="host_phenotype"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="cell_line"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="bio_material"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="target_gene"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="experimental_factor"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="identified_by"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="temperature"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> <option value="lower">lower</option> <option value="equal or lower">equal or lower</option> <option value="higher">higher</option> <option value="equal or higher">equal or higher</option> </param> <param name="value" type="float" value="" label="Any integer"/> </when> <when value="sampling_platform"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="collected_by"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="collection_date"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> <option value="lower">lower</option> <option value="equal or lower">equal or lower</option> <option value="higher">higher</option> <option value="equal or higher">equal or higher</option> </param> <param name="value" type="text" value="" label="A date in the format YYYY-MM-DD"/> </when> <when value="altitude"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> <option value="lower">lower</option> <option value="equal or lower">equal or lower</option> <option value="higher">higher</option> <option value="equal or higher">equal or higher</option> </param> <param name="value" type="float" value="" label="Any integer"/> </when> <when value="host_sex"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/> </when> <when value="investigation_type"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/> </when> <when value="location"> <conditional name="op"> <param name="operation" type="select" label="Operation"> <option value="geo_box2">All locations within a box defined by a centre point and a radius in km.</option> <option value="geo_box1">All locations within a box defined by the lower left (SW) and upper right (NE) points.</option> <option value="geo_circ">All locations within a circle defined by a centre point and a radius in km.</option> <option value="geo_lat">All locations within a latitude range given by a latitude and a radius in km.</option> <option value="geo_south">All locations south of a given latitude (inclusive).</option> <option value="geo_point">An exact lat/lon position</option> <option value="geo_north">All locations north of a given latitude (inclusive).</option> </param> <when value="geo_box2"> <param name="values" type="text" value="" label="latitude, longitude, radius (km)" help="Values separated by simple comma"/> </when> <when value="geo_box1"> <param name="values" type="text" value="" label="south-west latitude, south-west longitude, north-east latitude, north-east longitude" help="Values separated by simple comma"/> </when> <when value="geo_circ"> <param name="values" type="text" value="" label="latitude, longitude, radius (km)" help="Values separated by simple comma"/> </when> <when value="geo_lat"> <param name="values" type="text" value="" label="latitude, radius (km)" help="Values separated by simple comma"/> </when> <when value="geo_south"> <param name="values" type="text" value="" label="latitude" help="Values separated by simple comma"/> </when> <when value="geo_point"> <param name="values" type="text" value="" label="latitude, longitude" help="Values separated by simple comma"/> </when> <when value="geo_north"> <param name="values" type="text" value="" label="latitude" help="Values separated by simple comma"/> </when> </conditional> </when> <when value="host_genotype"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="ph"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> <option value="lower">lower</option> <option value="equal or lower">equal or lower</option> <option value="higher">higher</option> <option value="equal or higher">equal or higher</option> </param> <param name="value" type="float" value="" label="Any integer"/> </when> <when value="broker_name"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/> </when> <when value="project_name"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="elevation"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> <option value="lower">lower</option> <option value="equal or lower">equal or lower</option> <option value="higher">higher</option> <option value="equal or higher">equal or higher</option> </param> <param name="value" type="float" value="" label="Any integer"/> </when> <when value="description"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="sample_alias"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="checklist"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/> </when> <when value="sampling_campaign"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="protocol_label"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="isolation_source"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="sampling_site"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="host_tax_id"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> <option value="lower">lower</option> <option value="equal or lower">equal or lower</option> <option value="higher">higher</option> <option value="equal or higher">equal or higher</option> </param> <param name="value" type="float" value="" label="Any integer"/> </when> <when value="cultivar"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="environment_biome"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="environmental_package"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/> </when> <when value="marine_region"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="first_public"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> <option value="lower">lower</option> <option value="equal or lower">equal or lower</option> <option value="higher">higher</option> <option value="equal or higher">equal or higher</option> </param> <param name="value" type="text" value="" label="A date in the format YYYY-MM-DD"/> </when> <when value="environment_feature"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="country"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="host"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="salinity"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> <option value="lower">lower</option> <option value="equal or lower">equal or lower</option> <option value="higher">higher</option> <option value="equal or higher">equal or higher</option> </param> <param name="value" type="float" value="" label="Any integer"/> </when> <when value="host_status"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="strain"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="depth"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> <option value="lower">lower</option> <option value="equal or lower">equal or lower</option> <option value="higher">higher</option> <option value="equal or higher">equal or higher</option> </param> <param name="value" type="float" value="" label="Any integer"/> </when> <when value="tissue_type"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="host_body_site"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="host_growth_conditions"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="sample_collection"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="sequencing_method"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> </conditional> </repeat> <conditional name="display_opt"> <param argument="--display" type="select" label="Display option to specify the display format"> <expand macro="display_options"/> </param> <when value="xml"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> </when> <when value="text"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> </when> <when value="fastq"/> <when value="html"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> </when> <when value="report"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> <param argument="--fields" type="select" multiple="true" label="Fields to return"> <option value="accession">accession</option> <option value="secondary_sample_accession">secondary_sample_accession</option> <option value="bio_material">bio_material</option> <option value="cell_line">cell_line</option> <option value="collected_by">collected_by</option> <option value="collection_date">collection_date</option> <option value="country">country</option> <option value="marine_region">marine_region</option> <option value="cultivar">cultivar</option> <option value="description">description</option> <option value="dev_stage">dev_stage</option> <option value="first_public">first_public</option> <option value="identified_by">identified_by</option> <option value="isolation_source">isolation_source</option> <option value="location">location</option> <option value="strain">strain</option> <option value="tissue_type">tissue_type</option> <option value="tax_id">tax_id</option> <option value="scientific_name">scientific_name</option> <option value="sample_alias">sample_alias</option> <option value="checklist">checklist</option> <option value="center_name">center_name</option> <option value="depth">depth</option> <option value="elevation">elevation</option> <option value="altitude">altitude</option> <option value="environment_biome">environment_biome</option> <option value="environment_feature">environment_feature</option> <option value="environment_material">environment_material</option> <option value="temperature">temperature</option> <option value="salinity">salinity</option> <option value="sampling_campaign">sampling_campaign</option> <option value="sampling_site">sampling_site</option> <option value="sampling_platform">sampling_platform</option> <option value="protocol_label">protocol_label</option> <option value="project_name">project_name</option> <option value="host">host</option> <option value="host_tax_id">host_tax_id</option> <option value="host_status">host_status</option> <option value="host_sex">host_sex</option> <option value="submitted_host_sex">submitted_host_sex</option> <option value="host_body_site">host_body_site</option> <option value="host_gravidity">host_gravidity</option> <option value="host_phenotype">host_phenotype</option> <option value="host_genotype">host_genotype</option> <option value="host_growth_conditions">host_growth_conditions</option> <option value="environmental_package">environmental_package</option> <option value="investigation_type">investigation_type</option> <option value="experimental_factor">experimental_factor</option> <option value="sample_collection">sample_collection</option> <option value="sequencing_method">sequencing_method</option> <option value="target_gene">target_gene</option> <option value="ph">ph</option> <option value="broker_name">broker_name</option> <option value="event_label">event_label</option> </param> <param argument="--sortfields" type="select" optional="true" multiple="true" label="Fields to sort the results"> <option value="secondary_sample_accession">secondary sample accession number</option> <option value="environment_material">Environment (Material)</option> <option value="dev_stage">sample obtained from an organism in a specific developmental stage</option> <option value="event_label">label given to sampling event</option> <option value="center_name">Submitting center</option> <option value="accession">accession number</option> <option value="host_phenotype">phenotype of host</option> <option value="cell_line">cell line from which the sample was obtained</option> <option value="bio_material">identifier for biological material including institute and collection code</option> <option value="target_gene">targeted gene or locus name for marker gene studies</option> <option value="experimental_factor">variable aspects of the experimental design</option> <option value="identified_by">name of the taxonomist who identified the specimen</option> <option value="temperature">Temperature (C)</option> <option value="sampling_platform">the large infrastructure from which this sample was collected</option> <option value="collected_by">name of the person who collected the specimen</option> <option value="collection_date">date that the specimen was collected</option> <option value="altitude">Altitude (m)</option> <option value="host_sex">physical sex of the host</option> <option value="investigation_type">the study type targeted by the sequencing</option> <option value="location">geographic location of isolation of the sample</option> <option value="host_genotype">genotype of host</option> <option value="ph">pH</option> <option value="broker_name">broker name</option> <option value="project_name">name of the project within which the sequencing was organized</option> <option value="elevation">Elevation (m)</option> <option value="description">brief sequence description</option> <option value="sample_alias">submitter's name for the sample</option> <option value="checklist">checklist name (or ID)</option> <option value="sampling_campaign">the activity within which this sample was collected</option> <option value="protocol_label">the protocol used to produce the sample</option> <option value="isolation_source">describes the physical, environmental and/or local geographical source of the sample</option> <option value="sampling_site">the site/station where this sample was collection</option> <option value="host_tax_id">NCBI taxon id of the host</option> <option value="cultivar">cultivar (cultivated variety) of plant from which sample was obtained</option> <option value="environment_biome">Environment (Biome)</option> <option value="environmental_package">MIGS/MIMS/MIMARKS extension for reporting (from environment where the sample was obtained)</option> <option value="marine_region">geographical origin of the sample as defined by the marine region</option> <option value="first_public">date when made public</option> <option value="environment_feature">Environment (Feature)</option> <option value="country">locality of sample isolation: country names, oceans or seas, followed by regions and localities</option> <option value="host">natural (as opposed to laboratory) host to the organism from which sample was obtained</option> <option value="salinity">Salinity (PSU)</option> <option value="host_status">condition of host (eg. diseased or healthy)</option> <option value="strain">strain from which sample was obtained</option> <option value="depth">Depth (m)</option> <option value="tissue_type">tissue type from which the sample was obtained</option> <option value="host_body_site">name of body site from where the sample was obtained</option> <option value="host_growth_conditions">literature reference giving growth conditions of the host</option> <option value="sample_collection">the method or deviced employed for collecting the sample</option> <option value="sequencing_method">sequencing method used</option> </param> </when> <when value="fasta"/> </conditional> </when> <when value="read_run"> <repeat name="queries" title="Add a query"> <param name="combination_operation" type="select" label="Combination operation"> <option value="AND">AND</option> <option value="OR">OR</option> <option value="NOT">NOT</option> </param> <conditional name="filter_field"> <param name="field" type="select" label="Field to query"> <option value="secondary_sample_accession">secondary sample accession number</option> <option value="library_name">sequencing library name</option> <option value="read_count">number of reads</option> <option value="last_updated">date when last updated</option> <option value="center_name">Submitting center</option> <option value="submission_accession">submission accession number</option> <option value="nominal_length">average fragmentation size of paired reads</option> <option value="base_count">number of base pairs</option> <option value="run_accession">run accession number</option> <option value="library_selection">method used to select or enrich the material being sequenced</option> <option value="library_strategy">sequencing technique intended for the library</option> <option value="experiment_accession">experiment accession number</option> <option value="study_alias">submitter's name for the study</option> <option value="submitted_format"></option> <option value="broker_name">broker name</option> <option value="sample_alias">submitter's name for the sample</option> <option value="run_alias">submitter's name for the run</option> <option value="secondary_study_accession">project accession number</option> <option value="study_accession">study accession number</option> <option value="library_layout">sequencing library layout</option> <option value="library_source">source material being sequenced</option> <option value="experiment_title">brief experiment title</option> <option value="first_public">date when made public</option> <option value="instrument_platform">instrument platform used in sequencing experiment</option> <option value="instrument_model">instrument model used in sequencing experiment</option> <option value="sample_accession">sample accession number</option> <option value="experiment_alias">submitter's name for the experiment</option> <option value="study_title">brief sequencing study description</option> </param> <when value="secondary_sample_accession"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="library_name"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="read_count"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> <option value="lower">lower</option> <option value="equal or lower">equal or lower</option> <option value="higher">higher</option> <option value="equal or higher">equal or higher</option> </param> <param name="value" type="float" value="" label="Any integer"/> </when> <when value="last_updated"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> <option value="lower">lower</option> <option value="equal or lower">equal or lower</option> <option value="higher">higher</option> <option value="equal or higher">equal or higher</option> </param> <param name="value" type="text" value="" label="A date in the format YYYY-MM-DD"/> </when> <when value="center_name"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="submission_accession"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="nominal_length"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> <option value="lower">lower</option> <option value="equal or lower">equal or lower</option> <option value="higher">higher</option> <option value="equal or higher">equal or higher</option> </param> <param name="value" type="float" value="" label="Any integer"/> </when> <when value="base_count"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> <option value="lower">lower</option> <option value="equal or lower">equal or lower</option> <option value="higher">higher</option> <option value="equal or higher">equal or higher</option> </param> <param name="value" type="float" value="" label="Any integer"/> </when> <when value="run_accession"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="library_selection"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/> </when> <when value="library_strategy"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/> </when> <when value="experiment_accession"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="study_alias"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="submitted_format"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="broker_name"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/> </when> <when value="sample_alias"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="run_alias"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="secondary_study_accession"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="study_accession"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="library_layout"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/> </when> <when value="library_source"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/> </when> <when value="experiment_title"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="first_public"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> <option value="lower">lower</option> <option value="equal or lower">equal or lower</option> <option value="higher">higher</option> <option value="equal or higher">equal or higher</option> </param> <param name="value" type="text" value="" label="A date in the format YYYY-MM-DD"/> </when> <when value="instrument_platform"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/> </when> <when value="instrument_model"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/> </when> <when value="sample_accession"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="experiment_alias"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="study_title"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> </conditional> </repeat> <conditional name="display_opt"> <param argument="--display" type="select" label="Display option to specify the display format"> <expand macro="display_options"/> </param> <when value="xml"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> </when> <when value="text"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> </when> <when value="fastq"/> <when value="html"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> </when> <when value="report"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> <param argument="--fields" type="select" multiple="true" label="Fields to return"> <option value="study_accession">study_accession</option> <option value="secondary_study_accession">secondary_study_accession</option> <option value="sample_accession">sample_accession</option> <option value="secondary_sample_accession">secondary_sample_accession</option> <option value="experiment_accession">experiment_accession</option> <option value="run_accession">run_accession</option> <option value="submission_accession">submission_accession</option> <option value="tax_id">tax_id</option> <option value="scientific_name">scientific_name</option> <option value="instrument_platform">instrument_platform</option> <option value="instrument_model">instrument_model</option> <option value="library_name">library_name</option> <option value="nominal_length">nominal_length</option> <option value="library_layout">library_layout</option> <option value="library_strategy">library_strategy</option> <option value="library_source">library_source</option> <option value="library_selection">library_selection</option> <option value="read_count">read_count</option> <option value="base_count">base_count</option> <option value="center_name">center_name</option> <option value="first_public">first_public</option> <option value="last_updated">last_updated</option> <option value="experiment_title">experiment_title</option> <option value="study_title">study_title</option> <option value="study_alias">study_alias</option> <option value="experiment_alias">experiment_alias</option> <option value="run_alias">run_alias</option> <option value="fastq_bytes">fastq_bytes</option> <option value="fastq_md5">fastq_md5</option> <option value="fastq_ftp">fastq_ftp</option> <option value="fastq_aspera">fastq_aspera</option> <option value="fastq_galaxy">fastq_galaxy</option> <option value="submitted_bytes">submitted_bytes</option> <option value="submitted_md5">submitted_md5</option> <option value="submitted_ftp">submitted_ftp</option> <option value="submitted_aspera">submitted_aspera</option> <option value="submitted_galaxy">submitted_galaxy</option> <option value="submitted_format">submitted_format</option> <option value="sra_bytes">sra_bytes</option> <option value="sra_md5">sra_md5</option> <option value="sra_ftp">sra_ftp</option> <option value="sra_aspera">sra_aspera</option> <option value="sra_galaxy">sra_galaxy</option> <option value="cram_index_ftp">cram_index_ftp</option> <option value="cram_index_aspera">cram_index_aspera</option> <option value="cram_index_galaxy">cram_index_galaxy</option> <option value="sample_alias">sample_alias</option> <option value="broker_name">broker_name</option> </param> <param argument="--sortfields" type="select" optional="true" multiple="true" label="Fields to sort the results"> <option value="secondary_sample_accession">secondary sample accession number</option> <option value="library_name">sequencing library name</option> <option value="read_count">number of reads</option> <option value="last_updated">date when last updated</option> <option value="center_name">Submitting center</option> <option value="submission_accession">submission accession number</option> <option value="nominal_length">average fragmentation size of paired reads</option> <option value="base_count">number of base pairs</option> <option value="run_accession">run accession number</option> <option value="library_selection">method used to select or enrich the material being sequenced</option> <option value="library_strategy">sequencing technique intended for the library</option> <option value="experiment_accession">experiment accession number</option> <option value="study_alias">submitter's name for the study</option> <option value="submitted_format"></option> <option value="broker_name">broker name</option> <option value="sample_alias">submitter's name for the sample</option> <option value="run_alias">submitter's name for the run</option> <option value="secondary_study_accession">project accession number</option> <option value="study_accession">study accession number</option> <option value="library_layout">sequencing library layout</option> <option value="library_source">source material being sequenced</option> <option value="experiment_title">brief experiment title</option> <option value="first_public">date when made public</option> <option value="instrument_platform">instrument platform used in sequencing experiment</option> <option value="instrument_model">instrument model used in sequencing experiment</option> <option value="sample_accession">sample accession number</option> <option value="experiment_alias">submitter's name for the experiment</option> <option value="study_title">brief sequencing study description</option> </param> </when> <when value="fasta"/> </conditional> </when> <when value="read_study"> <repeat name="queries" title="Add a query"> <param name="combination_operation" type="select" label="Combination operation"> <option value="AND">AND</option> <option value="OR">OR</option> <option value="NOT">NOT</option> </param> <conditional name="filter_field"> <param name="field" type="select" label="Field to query"> <option value="study_title">brief sequencing study description</option> <option value="secondary_study_accession">project accession number</option> <option value="study_alias">submitter's name for the study</option> <option value="study_accession">study accession number</option> </param> <when value="study_title"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="secondary_study_accession"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="study_alias"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="study_accession"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> </conditional> </repeat> <conditional name="display_opt"> <param argument="--display" type="select" label="Display option to specify the display format"> <expand macro="display_options"/> </param> <when value="xml"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> </when> <when value="text"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> </when> <when value="fastq"/> <when value="html"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> </when> <when value="report"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> <param argument="--fields" type="select" multiple="true" label="Fields to return"> <option value="study_accession">study_accession</option> <option value="secondary_study_accession">secondary_study_accession</option> <option value="study_title">study_title</option> <option value="study_alias">study_alias</option> </param> <param argument="--sortfields" type="select" optional="true" multiple="true" label="Fields to sort the results"> <option value="study_title">brief sequencing study description</option> <option value="secondary_study_accession">project accession number</option> <option value="study_alias">submitter's name for the study</option> <option value="study_accession">study accession number</option> </param> </when> <when value="fasta"/> </conditional> </when> <when value="read_experiment"> <repeat name="queries" title="Add a query"> <param name="combination_operation" type="select" label="Combination operation"> <option value="AND">AND</option> <option value="OR">OR</option> <option value="NOT">NOT</option> </param> <conditional name="filter_field"> <param name="field" type="select" label="Field to query"> <option value="library_name">sequencing library name</option> <option value="study_title">brief sequencing study description</option> <option value="instrument_platform">instrument platform used in sequencing experiment</option> <option value="instrument_model">instrument model used in sequencing experiment</option> <option value="study_alias">submitter's name for the study</option> <option value="experiment_alias">submitter's name for the experiment</option> <option value="secondary_study_accession">project accession number</option> <option value="study_accession">study accession number</option> <option value="library_selection">method used to select or enrich the material being sequenced</option> <option value="library_layout">sequencing library layout</option> <option value="library_strategy">sequencing technique intended for the library</option> <option value="experiment_accession">experiment accession number</option> <option value="library_source">source material being sequenced</option> <option value="experiment_title">brief experiment title</option> </param> <when value="library_name"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="study_title"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="instrument_platform"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/> </when> <when value="instrument_model"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/> </when> <when value="study_alias"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="experiment_alias"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="secondary_study_accession"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="study_accession"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="library_selection"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/> </when> <when value="library_layout"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/> </when> <when value="library_strategy"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/> </when> <when value="experiment_accession"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="library_source"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/> </when> <when value="experiment_title"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> </conditional> </repeat> <conditional name="display_opt"> <param argument="--display" type="select" label="Display option to specify the display format"> <expand macro="display_options"/> </param> <when value="xml"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> </when> <when value="text"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> </when> <when value="fastq"/> <when value="html"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> </when> <when value="report"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> <param argument="--fields" type="select" multiple="true" label="Fields to return"> <option value="study_accession">study_accession</option> <option value="secondary_study_accession">secondary_study_accession</option> <option value="experiment_accession">experiment_accession</option> <option value="instrument_platform">instrument_platform</option> <option value="instrument_model">instrument_model</option> <option value="library_name">library_name</option> <option value="library_layout">library_layout</option> <option value="library_strategy">library_strategy</option> <option value="library_source">library_source</option> <option value="library_selection">library_selection</option> <option value="experiment_title">experiment_title</option> <option value="study_title">study_title</option> <option value="study_alias">study_alias</option> <option value="experiment_alias">experiment_alias</option> </param> <param argument="--sortfields" type="select" optional="true" multiple="true" label="Fields to sort the results"> <option value="library_name">sequencing library name</option> <option value="study_title">brief sequencing study description</option> <option value="instrument_platform">instrument platform used in sequencing experiment</option> <option value="instrument_model">instrument model used in sequencing experiment</option> <option value="study_alias">submitter's name for the study</option> <option value="experiment_alias">submitter's name for the experiment</option> <option value="secondary_study_accession">project accession number</option> <option value="study_accession">study accession number</option> <option value="library_selection">method used to select or enrich the material being sequenced</option> <option value="library_layout">sequencing library layout</option> <option value="library_strategy">sequencing technique intended for the library</option> <option value="experiment_accession">experiment accession number</option> <option value="library_source">source material being sequenced</option> <option value="experiment_title">brief experiment title</option> </param> </when> <when value="fasta"/> </conditional> </when> <when value="analysis"> <repeat name="queries" title="Add a query"> <param name="combination_operation" type="select" label="Combination operation"> <option value="AND">AND</option> <option value="OR">OR</option> <option value="NOT">NOT</option> </param> <conditional name="filter_field"> <param name="field" type="select" label="Field to query"> <option value="secondary_sample_accession">secondary sample accession number</option> <option value="broker_name">broker name</option> <option value="study_accession">study accession number</option> <option value="last_updated">date when last updated</option> <option value="first_public">date when made public</option> <option value="sample_alias">submitter's name for the sample</option> <option value="center_name">Submitting center</option> <option value="analysis_title">brief sequence analysis description</option> <option value="sample_accession">sample accession number</option> <option value="analysis_accession">analysis accession number</option> <option value="secondary_study_accession">project accession number</option> <option value="analysis_alias">submitter's name for the analysis</option> <option value="analysis_type">type of sequence analysis</option> <option value="study_title">brief sequencing study description</option> <option value="study_alias">submitter's name for the study</option> </param> <when value="secondary_sample_accession"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="broker_name"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/> </when> <when value="study_accession"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="last_updated"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> <option value="lower">lower</option> <option value="equal or lower">equal or lower</option> <option value="higher">higher</option> <option value="equal or higher">equal or higher</option> </param> <param name="value" type="text" value="" label="A date in the format YYYY-MM-DD"/> </when> <when value="first_public"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> <option value="lower">lower</option> <option value="equal or lower">equal or lower</option> <option value="higher">higher</option> <option value="equal or higher">equal or higher</option> </param> <param name="value" type="text" value="" label="A date in the format YYYY-MM-DD"/> </when> <when value="sample_alias"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="center_name"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="analysis_title"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="sample_accession"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="analysis_accession"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="secondary_study_accession"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="analysis_alias"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="analysis_type"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/> </when> <when value="study_title"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="study_alias"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> </conditional> </repeat> <conditional name="display_opt"> <param argument="--display" type="select" label="Display option to specify the display format"> <expand macro="display_options"/> </param> <when value="xml"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> </when> <when value="text"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> </when> <when value="fastq"/> <when value="html"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> </when> <when value="report"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> <param argument="--fields" type="select" multiple="true" label="Fields to return"> <option value="analysis_accession">analysis_accession</option> <option value="study_accession">study_accession</option> <option value="secondary_study_accession">secondary_study_accession</option> <option value="sample_accession">sample_accession</option> <option value="secondary_sample_accession">secondary_sample_accession</option> <option value="analysis_title">analysis_title</option> <option value="analysis_type">analysis_type</option> <option value="center_name">center_name</option> <option value="first_public">first_public</option> <option value="last_updated">last_updated</option> <option value="study_title">study_title</option> <option value="tax_id">tax_id</option> <option value="scientific_name">scientific_name</option> <option value="analysis_alias">analysis_alias</option> <option value="study_alias">study_alias</option> <option value="submitted_bytes">submitted_bytes</option> <option value="submitted_md5">submitted_md5</option> <option value="submitted_ftp">submitted_ftp</option> <option value="submitted_aspera">submitted_aspera</option> <option value="submitted_galaxy">submitted_galaxy</option> <option value="sample_alias">sample_alias</option> <option value="broker_name">broker_name</option> </param> <param argument="--sortfields" type="select" optional="true" multiple="true" label="Fields to sort the results"> <option value="secondary_sample_accession">secondary sample accession number</option> <option value="broker_name">broker name</option> <option value="study_accession">study accession number</option> <option value="last_updated">date when last updated</option> <option value="first_public">date when made public</option> <option value="sample_alias">submitter's name for the sample</option> <option value="center_name">Submitting center</option> <option value="analysis_title">brief sequence analysis description</option> <option value="sample_accession">sample accession number</option> <option value="analysis_accession">analysis accession number</option> <option value="secondary_study_accession">project accession number</option> <option value="analysis_alias">submitter's name for the analysis</option> <option value="analysis_type">type of sequence analysis</option> <option value="study_title">brief sequencing study description</option> <option value="study_alias">submitter's name for the study</option> </param> </when> <when value="fasta"/> </conditional> </when> <when value="sequence_update"> <repeat name="queries" title="Add a query"> <param name="combination_operation" type="select" label="Combination operation"> <option value="AND">AND</option> <option value="OR">OR</option> <option value="NOT">NOT</option> </param> <conditional name="filter_field"> <param name="field" type="select" label="Field to query"> <option value="mol_type">in vivo molecule type of the sequence</option> <option value="last_updated">date when last updated</option> <option value="sequence_md5"></option> <option value="haplotype">combination of alleles that are linked together on the same physical chromosome</option> <option value="serotype">serological variety of a species characterized by its antigenic properties</option> <option value="sex">sex of the organism from which the sample was obtained</option> <option value="keywords">keywords associated with sequence</option> <option value="collected_by">name of the person who collected the specimen</option> <option value="cell_line">cell line from which the sample was obtained</option> <option value="ecotype">a population within a given species displaying traits that reflect adaptation to a local habitat</option> <option value="bio_material">identifier for biological material including institute and collection code</option> <option value="identified_by">name of the taxonomist who identified the specimen</option> <option value="cell_type">cell type from which the sample was obtained</option> <option value="lab_host">scientific name of the laboratory host used to propagate the source organism for the sample</option> <option value="tax_division">taxonomic division</option> <option value="collection_date">date that the specimen was collected</option> <option value="specimen_voucher">identifier for the sample culture including institute and collection code</option> <option value="altitude">Altitude (m)</option> <option value="dev_stage">sample obtained from an organism in a specific developmental stage</option> <option value="isolate">individual isolate from which sample was obtained</option> <option value="location">geographic location of isolation of the sample</option> <option value="study_accession">study accession number</option> <option value="germline">the sample is an unrearranged molecule that was inherited from the parental germline</option> <option value="description">brief sequence description</option> <option value="accession">accession number</option> <option value="isolation_source">describes the physical, environmental and/or local geographical source of the sample</option> <option value="mating_type">mating type of the organism from which the sequence was obtained</option> <option value="tissue_type">tissue type from which the sample was obtained</option> <option value="sub_strain">name or identifier of a genetically or otherwise modified strain from which sample was obtained</option> <option value="tissue_lib">tissue library from which sample was obtained</option> <option value="cultivar">cultivar (cultivated variety) of plant from which sample was obtained</option> <option value="base_count">number of base pairs</option> <option value="topology">sequence topology: circular or linear</option> <option value="sub_species">name of sub-species of organism from which sample was obtained</option> <option value="environmental_sample">identifies sequences derived by direct molecular isolation from an environmental DNA sample</option> <option value="first_public">date when made public</option> <option value="strain">strain from which sample was obtained</option> <option value="country">locality of sample isolation: country names, oceans or seas, followed by regions and localities</option> <option value="variety">variety (varietas, a formal Linnaean rank) of organism from which sample was derived</option> <option value="host">natural (as opposed to laboratory) host to the organism from which sample was obtained</option> <option value="organelle">membrane-bound intracellular structure from which the sequence was obtained</option> <option value="serovar">serological variety of a species (usually a prokaryote) characterized by its antigenic properties</option> <option value="plasmid">name of naturally occurring plasmid from which the sequence was obtained</option> <option value="dataclass">sequence data class</option> <option value="culture_collection">identifier for the sample culture including institute and collection code</option> </param> <when value="mol_type"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/> </when> <when value="last_updated"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> <option value="lower">lower</option> <option value="equal or lower">equal or lower</option> <option value="higher">higher</option> <option value="equal or higher">equal or higher</option> </param> <param name="value" type="text" value="" label="A date in the format YYYY-MM-DD"/> </when> <when value="sequence_md5"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="haplotype"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="serotype"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="sex"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/> </when> <when value="keywords"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="collected_by"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="cell_line"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="ecotype"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="bio_material"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="identified_by"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="cell_type"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="lab_host"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="tax_division"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/> </when> <when value="collection_date"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> <option value="lower">lower</option> <option value="equal or lower">equal or lower</option> <option value="higher">higher</option> <option value="equal or higher">equal or higher</option> </param> <param name="value" type="text" value="" label="A date in the format YYYY-MM-DD"/> </when> <when value="specimen_voucher"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="altitude"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> <option value="lower">lower</option> <option value="equal or lower">equal or lower</option> <option value="higher">higher</option> <option value="equal or higher">equal or higher</option> </param> <param name="value" type="float" value="" label="Any integer"/> </when> <when value="dev_stage"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="isolate"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="location"> <conditional name="op"> <param name="operation" type="select" label="Operation"> <option value="geo_box2">All locations within a box defined by a centre point and a radius in km.</option> <option value="geo_box1">All locations within a box defined by the lower left (SW) and upper right (NE) points.</option> <option value="geo_circ">All locations within a circle defined by a centre point and a radius in km.</option> <option value="geo_lat">All locations within a latitude range given by a latitude and a radius in km.</option> <option value="geo_south">All locations south of a given latitude (inclusive).</option> <option value="geo_point">An exact lat/lon position</option> <option value="geo_north">All locations north of a given latitude (inclusive).</option> </param> <when value="geo_box2"> <param name="values" type="text" value="" label="latitude, longitude, radius (km)" help="Values separated by simple comma"/> </when> <when value="geo_box1"> <param name="values" type="text" value="" label="south-west latitude, south-west longitude, north-east latitude, north-east longitude" help="Values separated by simple comma"/> </when> <when value="geo_circ"> <param name="values" type="text" value="" label="latitude, longitude, radius (km)" help="Values separated by simple comma"/> </when> <when value="geo_lat"> <param name="values" type="text" value="" label="latitude, radius (km)" help="Values separated by simple comma"/> </when> <when value="geo_south"> <param name="values" type="text" value="" label="latitude" help="Values separated by simple comma"/> </when> <when value="geo_point"> <param name="values" type="text" value="" label="latitude, longitude" help="Values separated by simple comma"/> </when> <when value="geo_north"> <param name="values" type="text" value="" label="latitude" help="Values separated by simple comma"/> </when> </conditional> </when> <when value="study_accession"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="germline"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> </param> <param name="value" type="select" label="Value"> <option value="yes">yes</option> <option value="true">true</option> <option value="no">no</option> <option value="false">false</option> </param> </when> <when value="description"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="accession"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="isolation_source"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="mating_type"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="tissue_type"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="sub_strain"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="tissue_lib"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="cultivar"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="base_count"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> <option value="lower">lower</option> <option value="equal or lower">equal or lower</option> <option value="higher">higher</option> <option value="equal or higher">equal or higher</option> </param> <param name="value" type="float" value="" label="Any integer"/> </when> <when value="topology"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/> </when> <when value="sub_species"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="environmental_sample"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> </param> <param name="value" type="select" label="Value"> <option value="yes">yes</option> <option value="true">true</option> <option value="no">no</option> <option value="false">false</option> </param> </when> <when value="first_public"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> <option value="lower">lower</option> <option value="equal or lower">equal or lower</option> <option value="higher">higher</option> <option value="equal or higher">equal or higher</option> </param> <param name="value" type="text" value="" label="A date in the format YYYY-MM-DD"/> </when> <when value="strain"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="country"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="variety"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="host"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="organelle"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/> </when> <when value="serovar"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="plasmid"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="dataclass"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/> </when> <when value="culture_collection"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> </conditional> </repeat> <conditional name="display_opt"> <param argument="--display" type="select" label="Display option to specify the display format"> <expand macro="display_options"/> </param> <when value="xml"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> </when> <when value="text"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> </when> <when value="fastq"/> <when value="html"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> </when> <when value="report"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> <param argument="--fields" type="select" multiple="true" label="Fields to return"> <option value="accession">accession</option> <option value="base_count">base_count</option> <option value="bio_material">bio_material</option> <option value="cell_line">cell_line</option> <option value="cell_type">cell_type</option> <option value="collected_by">collected_by</option> <option value="collection_date">collection_date</option> <option value="country">country</option> <option value="cultivar">cultivar</option> <option value="culture_collection">culture_collection</option> <option value="dataclass">dataclass</option> <option value="description">description</option> <option value="dev_stage">dev_stage</option> <option value="ecotype">ecotype</option> <option value="environmental_sample">environmental_sample</option> <option value="first_public">first_public</option> <option value="germline">germline</option> <option value="host">host</option> <option value="identified_by">identified_by</option> <option value="isolate">isolate</option> <option value="isolation_source">isolation_source</option> <option value="keywords">keywords</option> <option value="lab_host">lab_host</option> <option value="last_updated">last_updated</option> <option value="location">location</option> <option value="mating_type">mating_type</option> <option value="mol_type">mol_type</option> <option value="organelle">organelle</option> <option value="serotype">serotype</option> <option value="serovar">serovar</option> <option value="sex">sex</option> <option value="submitted_sex">submitted_sex</option> <option value="specimen_voucher">specimen_voucher</option> <option value="strain">strain</option> <option value="sub_species">sub_species</option> <option value="sub_strain">sub_strain</option> <option value="tax_division">tax_division</option> <option value="tissue_lib">tissue_lib</option> <option value="tissue_type">tissue_type</option> <option value="topology">topology</option> <option value="variety">variety</option> <option value="tax_id">tax_id</option> <option value="scientific_name">scientific_name</option> <option value="altitude">altitude</option> <option value="haplotype">haplotype</option> <option value="plasmid">plasmid</option> <option value="study_accession">study_accession</option> <option value="sequence_md5">sequence_md5</option> </param> <param argument="--sortfields" type="select" optional="true" multiple="true" label="Fields to sort the results"> <option value="mol_type">in vivo molecule type of the sequence</option> <option value="last_updated">date when last updated</option> <option value="sequence_md5"></option> <option value="haplotype">combination of alleles that are linked together on the same physical chromosome</option> <option value="serotype">serological variety of a species characterized by its antigenic properties</option> <option value="sex">sex of the organism from which the sample was obtained</option> <option value="keywords">keywords associated with sequence</option> <option value="collected_by">name of the person who collected the specimen</option> <option value="cell_line">cell line from which the sample was obtained</option> <option value="ecotype">a population within a given species displaying traits that reflect adaptation to a local habitat</option> <option value="bio_material">identifier for biological material including institute and collection code</option> <option value="identified_by">name of the taxonomist who identified the specimen</option> <option value="cell_type">cell type from which the sample was obtained</option> <option value="lab_host">scientific name of the laboratory host used to propagate the source organism for the sample</option> <option value="tax_division">taxonomic division</option> <option value="collection_date">date that the specimen was collected</option> <option value="specimen_voucher">identifier for the sample culture including institute and collection code</option> <option value="altitude">Altitude (m)</option> <option value="dev_stage">sample obtained from an organism in a specific developmental stage</option> <option value="isolate">individual isolate from which sample was obtained</option> <option value="location">geographic location of isolation of the sample</option> <option value="study_accession">study accession number</option> <option value="germline">the sample is an unrearranged molecule that was inherited from the parental germline</option> <option value="description">brief sequence description</option> <option value="accession">accession number</option> <option value="isolation_source">describes the physical, environmental and/or local geographical source of the sample</option> <option value="mating_type">mating type of the organism from which the sequence was obtained</option> <option value="tissue_type">tissue type from which the sample was obtained</option> <option value="sub_strain">name or identifier of a genetically or otherwise modified strain from which sample was obtained</option> <option value="tissue_lib">tissue library from which sample was obtained</option> <option value="cultivar">cultivar (cultivated variety) of plant from which sample was obtained</option> <option value="base_count">number of base pairs</option> <option value="topology">sequence topology: circular or linear</option> <option value="sub_species">name of sub-species of organism from which sample was obtained</option> <option value="environmental_sample">identifies sequences derived by direct molecular isolation from an environmental DNA sample</option> <option value="first_public">date when made public</option> <option value="strain">strain from which sample was obtained</option> <option value="country">locality of sample isolation: country names, oceans or seas, followed by regions and localities</option> <option value="variety">variety (varietas, a formal Linnaean rank) of organism from which sample was derived</option> <option value="host">natural (as opposed to laboratory) host to the organism from which sample was obtained</option> <option value="organelle">membrane-bound intracellular structure from which the sequence was obtained</option> <option value="serovar">serological variety of a species (usually a prokaryote) characterized by its antigenic properties</option> <option value="plasmid">name of naturally occurring plasmid from which the sequence was obtained</option> <option value="dataclass">sequence data class</option> <option value="culture_collection">identifier for the sample culture including institute and collection code</option> </param> </when> <when value="fasta"/> </conditional> </when> <when value="coding_update"> <repeat name="queries" title="Add a query"> <param name="combination_operation" type="select" label="Combination operation"> <option value="AND">AND</option> <option value="OR">OR</option> <option value="NOT">NOT</option> </param> <conditional name="filter_field"> <param name="field" type="select" label="Field to query"> <option value="operon">name of the group of contiguous genes transcribed into a single transcript</option> <option value="mol_type">in vivo molecule type of the sequence</option> <option value="last_updated">date when last updated</option> <option value="lab_host">scientific name of the laboratory host used to propagate the source organism for the sample</option> <option value="transl_except">a single codon translation that does not conform to genetic code</option> <option value="haplotype">combination of alleles that are linked together on the same physical chromosome</option> <option value="serotype">serological variety of a species characterized by its antigenic properties</option> <option value="trans_splicing">indicates exons from two RNA molecules are ligated in intermolecular reaction to form mature RNA</option> <option value="sex">sex of the organism from which the sample was obtained</option> <option value="pseudo_gene">indicates that this feature is a pseudogene</option> <option value="standard_name">accepted standard name for a feature</option> <option value="collected_by">name of the person who collected the specimen</option> <option value="germline">the sample is an unrearranged molecule that was inherited from the parental germline</option> <option value="cell_type">cell type from which the sample was obtained</option> <option value="host">natural (as opposed to laboratory) host to the organism from which sample was obtained</option> <option value="inference">a structured description of non-experimental evidence</option> <option value="bio_material">identifier for biological material including institute and collection code</option> <option value="parent_accession">parent sequence accession number</option> <option value="identified_by">name of the taxonomist who identified the specimen</option> <option value="locus_tag">a submitter-supplied, systematic, stable identifier for a gene and its associated features</option> <option value="sequence_md5"></option> <option value="tax_division">taxonomic division</option> <option value="old_locus_tag">deprecated submitter-supplied, systematic, stable identifier for a gene and its associated features</option> <option value="specimen_voucher">identifier for the sample culture including institute and collection code</option> <option value="altitude">Altitude (m)</option> <option value="dev_stage">sample obtained from an organism in a specific developmental stage</option> <option value="isolate">individual isolate from which sample was obtained</option> <option value="ec_number">Enzyme Commission number for enzyme product of sequence</option> <option value="note">any comment or additional information</option> <option value="experiment">a brief description of the nature of the experimental evidence</option> <option value="location">geographic location of isolation of the sample</option> <option value="collection_date">date that the specimen was collected</option> <option value="allele">name of the allele for the given gene</option> <option value="protein_id">a stable protein identifier issued by INSDC</option> <option value="partial">differentiates between complete regions and partial ones (deprecated qualifier)</option> <option value="artificial_location">indicates location is modified to adjust for the presence of a frameshift or internal stop codon</option> <option value="function">function attributed to a sequence</option> <option value="map">genomic map position of feature</option> <option value="product">name of the product associated with the feature</option> <option value="description">brief sequence description</option> <option value="cell_line">cell line from which the sample was obtained</option> <option value="gene_synonym">synonymous, replaced, obsolete or former gene symbol</option> <option value="ecotype">a population within a given species displaying traits that reflect adaptation to a local habitat</option> <option value="exception">indicates that the coding region cannot be translated using standard biological rules</option> <option value="accession">accession number</option> <option value="isolation_source">describes the physical, environmental and/or local geographical source of the sample</option> <option value="mating_type">mating type of the organism from which the sequence was obtained</option> <option value="tissue_type">tissue type from which the sample was obtained</option> <option value="sub_strain">name or identifier of a genetically or otherwise modified strain from which sample was obtained</option> <option value="tissue_lib">tissue library from which sample was obtained</option> <option value="cultivar">cultivar (cultivated variety) of plant from which sample was obtained</option> <option value="base_count">number of base pairs</option> <option value="topology">sequence topology: circular or linear</option> <option value="sub_species">name of sub-species of organism from which sample was obtained</option> <option value="first_public">date when made public</option> <option value="strain">strain from which sample was obtained</option> <option value="country">locality of sample isolation: country names, oceans or seas, followed by regions and localities</option> <option value="variety">variety (varietas, a formal Linnaean rank) of organism from which sample was derived</option> <option value="pseudo">the feature is non-functional</option> <option value="environmental_sample">identifies sequences derived by direct molecular isolation from an environmental DNA sample</option> <option value="transl_table">indicates the genetic code table used if other than universal genetic code table</option> <option value="organelle">membrane-bound intracellular structure from which the sequence was obtained</option> <option value="ribosomal_slippage">indicates ribosomal slippage (change to an alternative reading frame) during protein translation</option> <option value="serovar">serological variety of a species (usually a prokaryote) characterized by its antigenic properties</option> <option value="keywords">keywords associated with sequence</option> <option value="dataclass">sequence data class</option> <option value="gene">symbol of the gene corresponding to a sequence region</option> <option value="codon_start">indicates the offset of the first complete codon relative to the first base of the coding feature</option> <option value="culture_collection">identifier for the sample culture including institute and collection code</option> </param> <when value="operon"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="mol_type"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/> </when> <when value="last_updated"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> <option value="lower">lower</option> <option value="equal or lower">equal or lower</option> <option value="higher">higher</option> <option value="equal or higher">equal or higher</option> </param> <param name="value" type="text" value="" label="A date in the format YYYY-MM-DD"/> </when> <when value="lab_host"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="transl_except"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="haplotype"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="serotype"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="trans_splicing"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> </param> <param name="value" type="select" label="Value"> <option value="yes">yes</option> <option value="true">true</option> <option value="no">no</option> <option value="false">false</option> </param> </when> <when value="sex"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/> </when> <when value="pseudo_gene"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/> </when> <when value="standard_name"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="collected_by"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="germline"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> </param> <param name="value" type="select" label="Value"> <option value="yes">yes</option> <option value="true">true</option> <option value="no">no</option> <option value="false">false</option> </param> </when> <when value="cell_type"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="host"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="inference"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="bio_material"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="parent_accession"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="identified_by"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="locus_tag"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="sequence_md5"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="tax_division"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/> </when> <when value="old_locus_tag"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="specimen_voucher"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="altitude"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> <option value="lower">lower</option> <option value="equal or lower">equal or lower</option> <option value="higher">higher</option> <option value="equal or higher">equal or higher</option> </param> <param name="value" type="float" value="" label="Any integer"/> </when> <when value="dev_stage"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="isolate"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="ec_number"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="note"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="experiment"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="location"> <conditional name="op"> <param name="operation" type="select" label="Operation"> <option value="geo_box2">All locations within a box defined by a centre point and a radius in km.</option> <option value="geo_box1">All locations within a box defined by the lower left (SW) and upper right (NE) points.</option> <option value="geo_circ">All locations within a circle defined by a centre point and a radius in km.</option> <option value="geo_lat">All locations within a latitude range given by a latitude and a radius in km.</option> <option value="geo_south">All locations south of a given latitude (inclusive).</option> <option value="geo_point">An exact lat/lon position</option> <option value="geo_north">All locations north of a given latitude (inclusive).</option> </param> <when value="geo_box2"> <param name="values" type="text" value="" label="latitude, longitude, radius (km)" help="Values separated by simple comma"/> </when> <when value="geo_box1"> <param name="values" type="text" value="" label="south-west latitude, south-west longitude, north-east latitude, north-east longitude" help="Values separated by simple comma"/> </when> <when value="geo_circ"> <param name="values" type="text" value="" label="latitude, longitude, radius (km)" help="Values separated by simple comma"/> </when> <when value="geo_lat"> <param name="values" type="text" value="" label="latitude, radius (km)" help="Values separated by simple comma"/> </when> <when value="geo_south"> <param name="values" type="text" value="" label="latitude" help="Values separated by simple comma"/> </when> <when value="geo_point"> <param name="values" type="text" value="" label="latitude, longitude" help="Values separated by simple comma"/> </when> <when value="geo_north"> <param name="values" type="text" value="" label="latitude" help="Values separated by simple comma"/> </when> </conditional> </when> <when value="collection_date"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> <option value="lower">lower</option> <option value="equal or lower">equal or lower</option> <option value="higher">higher</option> <option value="equal or higher">equal or higher</option> </param> <param name="value" type="text" value="" label="A date in the format YYYY-MM-DD"/> </when> <when value="allele"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="protein_id"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="partial"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> </param> <param name="value" type="select" label="Value"> <option value="yes">yes</option> <option value="true">true</option> <option value="no">no</option> <option value="false">false</option> </param> </when> <when value="artificial_location"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/> </when> <when value="function"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="map"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="product"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="description"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="cell_line"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="gene_synonym"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="ecotype"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="exception"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="accession"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="isolation_source"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="mating_type"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="tissue_type"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="sub_strain"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="tissue_lib"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="cultivar"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="base_count"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> <option value="lower">lower</option> <option value="equal or lower">equal or lower</option> <option value="higher">higher</option> <option value="equal or higher">equal or higher</option> </param> <param name="value" type="float" value="" label="Any integer"/> </when> <when value="topology"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/> </when> <when value="sub_species"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="first_public"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> <option value="lower">lower</option> <option value="equal or lower">equal or lower</option> <option value="higher">higher</option> <option value="equal or higher">equal or higher</option> </param> <param name="value" type="text" value="" label="A date in the format YYYY-MM-DD"/> </when> <when value="strain"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="country"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="variety"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="pseudo"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> </param> <param name="value" type="select" label="Value"> <option value="yes">yes</option> <option value="true">true</option> <option value="no">no</option> <option value="false">false</option> </param> </when> <when value="environmental_sample"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> </param> <param name="value" type="select" label="Value"> <option value="yes">yes</option> <option value="true">true</option> <option value="no">no</option> <option value="false">false</option> </param> </when> <when value="transl_table"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/> </when> <when value="organelle"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/> </when> <when value="ribosomal_slippage"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> </param> <param name="value" type="select" label="Value"> <option value="yes">yes</option> <option value="true">true</option> <option value="no">no</option> <option value="false">false</option> </param> </when> <when value="serovar"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="keywords"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="dataclass"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/> </when> <when value="gene"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="codon_start"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/> </when> <when value="culture_collection"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> </conditional> </repeat> <conditional name="display_opt"> <param argument="--display" type="select" label="Display option to specify the display format"> <expand macro="display_options"/> </param> <when value="xml"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> </when> <when value="text"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> </when> <when value="fastq"/> <when value="html"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> </when> <when value="report"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> <param argument="--fields" type="select" multiple="true" label="Fields to return"> <option value="accession">accession</option> <option value="base_count">base_count</option> <option value="bio_material">bio_material</option> <option value="cell_line">cell_line</option> <option value="cell_type">cell_type</option> <option value="collected_by">collected_by</option> <option value="collection_date">collection_date</option> <option value="country">country</option> <option value="cultivar">cultivar</option> <option value="culture_collection">culture_collection</option> <option value="dataclass">dataclass</option> <option value="description">description</option> <option value="dev_stage">dev_stage</option> <option value="ecotype">ecotype</option> <option value="environmental_sample">environmental_sample</option> <option value="first_public">first_public</option> <option value="germline">germline</option> <option value="host">host</option> <option value="identified_by">identified_by</option> <option value="isolate">isolate</option> <option value="isolation_source">isolation_source</option> <option value="keywords">keywords</option> <option value="lab_host">lab_host</option> <option value="last_updated">last_updated</option> <option value="location">location</option> <option value="mating_type">mating_type</option> <option value="mol_type">mol_type</option> <option value="organelle">organelle</option> <option value="serotype">serotype</option> <option value="serovar">serovar</option> <option value="sex">sex</option> <option value="submitted_sex">submitted_sex</option> <option value="specimen_voucher">specimen_voucher</option> <option value="strain">strain</option> <option value="sub_species">sub_species</option> <option value="sub_strain">sub_strain</option> <option value="tax_division">tax_division</option> <option value="tissue_lib">tissue_lib</option> <option value="tissue_type">tissue_type</option> <option value="variety">variety</option> <option value="allele">allele</option> <option value="artificial_location">artificial_location</option> <option value="codon_start">codon_start</option> <option value="ec_number">ec_number</option> <option value="exception">exception</option> <option value="experiment">experiment</option> <option value="function">function</option> <option value="topology">topology</option> <option value="gene">gene</option> <option value="gene_synonym">gene_synonym</option> <option value="inference">inference</option> <option value="locus_tag">locus_tag</option> <option value="map">map</option> <option value="note">note</option> <option value="old_locus_tag">old_locus_tag</option> <option value="operon">operon</option> <option value="partial">partial</option> <option value="product">product</option> <option value="protein_id">protein_id</option> <option value="pseudo">pseudo</option> <option value="pseudo_gene">pseudo_gene</option> <option value="ribosomal_slippage">ribosomal_slippage</option> <option value="standard_name">standard_name</option> <option value="trans_splicing">trans_splicing</option> <option value="transl_except">transl_except</option> <option value="transl_table">transl_table</option> <option value="tax_id">tax_id</option> <option value="scientific_name">scientific_name</option> <option value="parent_accession">parent_accession</option> <option value="altitude">altitude</option> <option value="haplotype">haplotype</option> <option value="sequence_md5">sequence_md5</option> </param> <param argument="--sortfields" type="select" optional="true" multiple="true" label="Fields to sort the results"> <option value="operon">name of the group of contiguous genes transcribed into a single transcript</option> <option value="mol_type">in vivo molecule type of the sequence</option> <option value="last_updated">date when last updated</option> <option value="lab_host">scientific name of the laboratory host used to propagate the source organism for the sample</option> <option value="transl_except">a single codon translation that does not conform to genetic code</option> <option value="haplotype">combination of alleles that are linked together on the same physical chromosome</option> <option value="serotype">serological variety of a species characterized by its antigenic properties</option> <option value="trans_splicing">indicates exons from two RNA molecules are ligated in intermolecular reaction to form mature RNA</option> <option value="sex">sex of the organism from which the sample was obtained</option> <option value="pseudo_gene">indicates that this feature is a pseudogene</option> <option value="standard_name">accepted standard name for a feature</option> <option value="collected_by">name of the person who collected the specimen</option> <option value="germline">the sample is an unrearranged molecule that was inherited from the parental germline</option> <option value="cell_type">cell type from which the sample was obtained</option> <option value="host">natural (as opposed to laboratory) host to the organism from which sample was obtained</option> <option value="inference">a structured description of non-experimental evidence</option> <option value="bio_material">identifier for biological material including institute and collection code</option> <option value="parent_accession">parent sequence accession number</option> <option value="identified_by">name of the taxonomist who identified the specimen</option> <option value="locus_tag">a submitter-supplied, systematic, stable identifier for a gene and its associated features</option> <option value="sequence_md5"></option> <option value="tax_division">taxonomic division</option> <option value="old_locus_tag">deprecated submitter-supplied, systematic, stable identifier for a gene and its associated features</option> <option value="specimen_voucher">identifier for the sample culture including institute and collection code</option> <option value="altitude">Altitude (m)</option> <option value="dev_stage">sample obtained from an organism in a specific developmental stage</option> <option value="isolate">individual isolate from which sample was obtained</option> <option value="ec_number">Enzyme Commission number for enzyme product of sequence</option> <option value="note">any comment or additional information</option> <option value="experiment">a brief description of the nature of the experimental evidence</option> <option value="location">geographic location of isolation of the sample</option> <option value="collection_date">date that the specimen was collected</option> <option value="allele">name of the allele for the given gene</option> <option value="protein_id">a stable protein identifier issued by INSDC</option> <option value="partial">differentiates between complete regions and partial ones (deprecated qualifier)</option> <option value="artificial_location">indicates location is modified to adjust for the presence of a frameshift or internal stop codon</option> <option value="function">function attributed to a sequence</option> <option value="map">genomic map position of feature</option> <option value="product">name of the product associated with the feature</option> <option value="description">brief sequence description</option> <option value="cell_line">cell line from which the sample was obtained</option> <option value="gene_synonym">synonymous, replaced, obsolete or former gene symbol</option> <option value="ecotype">a population within a given species displaying traits that reflect adaptation to a local habitat</option> <option value="exception">indicates that the coding region cannot be translated using standard biological rules</option> <option value="accession">accession number</option> <option value="isolation_source">describes the physical, environmental and/or local geographical source of the sample</option> <option value="mating_type">mating type of the organism from which the sequence was obtained</option> <option value="tissue_type">tissue type from which the sample was obtained</option> <option value="sub_strain">name or identifier of a genetically or otherwise modified strain from which sample was obtained</option> <option value="tissue_lib">tissue library from which sample was obtained</option> <option value="cultivar">cultivar (cultivated variety) of plant from which sample was obtained</option> <option value="base_count">number of base pairs</option> <option value="topology">sequence topology: circular or linear</option> <option value="sub_species">name of sub-species of organism from which sample was obtained</option> <option value="first_public">date when made public</option> <option value="strain">strain from which sample was obtained</option> <option value="country">locality of sample isolation: country names, oceans or seas, followed by regions and localities</option> <option value="variety">variety (varietas, a formal Linnaean rank) of organism from which sample was derived</option> <option value="pseudo">the feature is non-functional</option> <option value="environmental_sample">identifies sequences derived by direct molecular isolation from an environmental DNA sample</option> <option value="transl_table">indicates the genetic code table used if other than universal genetic code table</option> <option value="organelle">membrane-bound intracellular structure from which the sequence was obtained</option> <option value="ribosomal_slippage">indicates ribosomal slippage (change to an alternative reading frame) during protein translation</option> <option value="serovar">serological variety of a species (usually a prokaryote) characterized by its antigenic properties</option> <option value="keywords">keywords associated with sequence</option> <option value="dataclass">sequence data class</option> <option value="gene">symbol of the gene corresponding to a sequence region</option> <option value="codon_start">indicates the offset of the first complete codon relative to the first base of the coding feature</option> <option value="culture_collection">identifier for the sample culture including institute and collection code</option> </param> </when> <when value="fasta"/> </conditional> </when> <when value="tsa_set"> <repeat name="queries" title="Add a query"> <param name="combination_operation" type="select" label="Combination operation"> <option value="AND">AND</option> <option value="OR">OR</option> <option value="NOT">NOT</option> </param> <conditional name="filter_field"> <param name="field" type="select" label="Field to query"> <option value="mol_type">in vivo molecule type of the sequence</option> <option value="last_updated">date when last updated</option> <option value="lab_host">scientific name of the laboratory host used to propagate the source organism for the sample</option> <option value="haplotype">combination of alleles that are linked together on the same physical chromosome</option> <option value="accession">accession number</option> <option value="sex">sex of the organism from which the sample was obtained</option> <option value="cell_line">cell line from which the sample was obtained</option> <option value="host">natural (as opposed to laboratory) host to the organism from which sample was obtained</option> <option value="ecotype">a population within a given species displaying traits that reflect adaptation to a local habitat</option> <option value="bio_material">identifier for biological material including institute and collection code</option> <option value="identified_by">name of the taxonomist who identified the specimen</option> <option value="cell_type">cell type from which the sample was obtained</option> <option value="tax_division">taxonomic division</option> <option value="collection_date">date that the specimen was collected</option> <option value="specimen_voucher">identifier for the sample culture including institute and collection code</option> <option value="altitude">Altitude (m)</option> <option value="dev_stage">sample obtained from an organism in a specific developmental stage</option> <option value="isolate">individual isolate from which sample was obtained</option> <option value="location">geographic location of isolation of the sample</option> <option value="study_accession">study accession number</option> <option value="germline">the sample is an unrearranged molecule that was inherited from the parental germline</option> <option value="description">brief sequence description</option> <option value="tissue_lib">tissue library from which sample was obtained</option> <option value="isolation_source">describes the physical, environmental and/or local geographical source of the sample</option> <option value="mating_type">mating type of the organism from which the sequence was obtained</option> <option value="serovar">serological variety of a species (usually a prokaryote) characterized by its antigenic properties</option> <option value="serotype">serological variety of a species characterized by its antigenic properties</option> <option value="sub_strain">name or identifier of a genetically or otherwise modified strain from which sample was obtained</option> <option value="cultivar">cultivar (cultivated variety) of plant from which sample was obtained</option> <option value="collected_by">name of the person who collected the specimen</option> <option value="sub_species">name of sub-species of organism from which sample was obtained</option> <option value="first_public">date when made public</option> <option value="strain">strain from which sample was obtained</option> <option value="country">locality of sample isolation: country names, oceans or seas, followed by regions and localities</option> <option value="variety">variety (varietas, a formal Linnaean rank) of organism from which sample was derived</option> <option value="environmental_sample">identifies sequences derived by direct molecular isolation from an environmental DNA sample</option> <option value="tissue_type">tissue type from which the sample was obtained</option> <option value="keywords">keywords associated with sequence</option> <option value="culture_collection">identifier for the sample culture including institute and collection code</option> </param> <when value="mol_type"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/> </when> <when value="last_updated"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> <option value="lower">lower</option> <option value="equal or lower">equal or lower</option> <option value="higher">higher</option> <option value="equal or higher">equal or higher</option> </param> <param name="value" type="text" value="" label="A date in the format YYYY-MM-DD"/> </when> <when value="lab_host"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="haplotype"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="accession"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="sex"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/> </when> <when value="cell_line"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="host"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="ecotype"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="bio_material"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="identified_by"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="cell_type"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="tax_division"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/> </when> <when value="collection_date"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> <option value="lower">lower</option> <option value="equal or lower">equal or lower</option> <option value="higher">higher</option> <option value="equal or higher">equal or higher</option> </param> <param name="value" type="text" value="" label="A date in the format YYYY-MM-DD"/> </when> <when value="specimen_voucher"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="altitude"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> <option value="lower">lower</option> <option value="equal or lower">equal or lower</option> <option value="higher">higher</option> <option value="equal or higher">equal or higher</option> </param> <param name="value" type="float" value="" label="Any integer"/> </when> <when value="dev_stage"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="isolate"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="location"> <conditional name="op"> <param name="operation" type="select" label="Operation"> <option value="geo_box2">All locations within a box defined by a centre point and a radius in km.</option> <option value="geo_box1">All locations within a box defined by the lower left (SW) and upper right (NE) points.</option> <option value="geo_circ">All locations within a circle defined by a centre point and a radius in km.</option> <option value="geo_lat">All locations within a latitude range given by a latitude and a radius in km.</option> <option value="geo_south">All locations south of a given latitude (inclusive).</option> <option value="geo_point">An exact lat/lon position</option> <option value="geo_north">All locations north of a given latitude (inclusive).</option> </param> <when value="geo_box2"> <param name="values" type="text" value="" label="latitude, longitude, radius (km)" help="Values separated by simple comma"/> </when> <when value="geo_box1"> <param name="values" type="text" value="" label="south-west latitude, south-west longitude, north-east latitude, north-east longitude" help="Values separated by simple comma"/> </when> <when value="geo_circ"> <param name="values" type="text" value="" label="latitude, longitude, radius (km)" help="Values separated by simple comma"/> </when> <when value="geo_lat"> <param name="values" type="text" value="" label="latitude, radius (km)" help="Values separated by simple comma"/> </when> <when value="geo_south"> <param name="values" type="text" value="" label="latitude" help="Values separated by simple comma"/> </when> <when value="geo_point"> <param name="values" type="text" value="" label="latitude, longitude" help="Values separated by simple comma"/> </when> <when value="geo_north"> <param name="values" type="text" value="" label="latitude" help="Values separated by simple comma"/> </when> </conditional> </when> <when value="study_accession"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="germline"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> </param> <param name="value" type="select" label="Value"> <option value="yes">yes</option> <option value="true">true</option> <option value="no">no</option> <option value="false">false</option> </param> </when> <when value="description"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="tissue_lib"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="isolation_source"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="mating_type"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="serovar"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="serotype"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="sub_strain"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="cultivar"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="collected_by"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="sub_species"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="first_public"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> <option value="lower">lower</option> <option value="equal or lower">equal or lower</option> <option value="higher">higher</option> <option value="equal or higher">equal or higher</option> </param> <param name="value" type="text" value="" label="A date in the format YYYY-MM-DD"/> </when> <when value="strain"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="country"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="variety"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="environmental_sample"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> </param> <param name="value" type="select" label="Value"> <option value="yes">yes</option> <option value="true">true</option> <option value="no">no</option> <option value="false">false</option> </param> </when> <when value="tissue_type"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="keywords"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="culture_collection"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> </conditional> </repeat> <conditional name="display_opt"> <param argument="--display" type="select" label="Display option to specify the display format"> <expand macro="display_options"/> </param> <when value="xml"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> </when> <when value="text"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> </when> <when value="fastq"/> <when value="html"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> </when> <when value="report"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> <param argument="--fields" type="select" multiple="true" label="Fields to return"> <option value="accession">accession</option> <option value="bio_material">bio_material</option> <option value="cell_line">cell_line</option> <option value="cell_type">cell_type</option> <option value="collected_by">collected_by</option> <option value="collection_date">collection_date</option> <option value="country">country</option> <option value="cultivar">cultivar</option> <option value="culture_collection">culture_collection</option> <option value="description">description</option> <option value="dev_stage">dev_stage</option> <option value="ecotype">ecotype</option> <option value="environmental_sample">environmental_sample</option> <option value="first_public">first_public</option> <option value="germline">germline</option> <option value="host">host</option> <option value="identified_by">identified_by</option> <option value="isolate">isolate</option> <option value="isolation_source">isolation_source</option> <option value="keywords">keywords</option> <option value="lab_host">lab_host</option> <option value="last_updated">last_updated</option> <option value="location">location</option> <option value="mating_type">mating_type</option> <option value="mol_type">mol_type</option> <option value="serotype">serotype</option> <option value="serovar">serovar</option> <option value="sex">sex</option> <option value="submitted_sex">submitted_sex</option> <option value="specimen_voucher">specimen_voucher</option> <option value="strain">strain</option> <option value="sub_species">sub_species</option> <option value="sub_strain">sub_strain</option> <option value="tax_division">tax_division</option> <option value="tissue_lib">tissue_lib</option> <option value="tissue_type">tissue_type</option> <option value="variety">variety</option> <option value="tax_id">tax_id</option> <option value="scientific_name">scientific_name</option> <option value="altitude">altitude</option> <option value="haplotype">haplotype</option> <option value="study_accession">study_accession</option> <option value="set_files">set_files</option> </param> <param argument="--sortfields" type="select" optional="true" multiple="true" label="Fields to sort the results"> <option value="mol_type">in vivo molecule type of the sequence</option> <option value="last_updated">date when last updated</option> <option value="lab_host">scientific name of the laboratory host used to propagate the source organism for the sample</option> <option value="haplotype">combination of alleles that are linked together on the same physical chromosome</option> <option value="accession">accession number</option> <option value="sex">sex of the organism from which the sample was obtained</option> <option value="cell_line">cell line from which the sample was obtained</option> <option value="host">natural (as opposed to laboratory) host to the organism from which sample was obtained</option> <option value="ecotype">a population within a given species displaying traits that reflect adaptation to a local habitat</option> <option value="bio_material">identifier for biological material including institute and collection code</option> <option value="identified_by">name of the taxonomist who identified the specimen</option> <option value="cell_type">cell type from which the sample was obtained</option> <option value="tax_division">taxonomic division</option> <option value="collection_date">date that the specimen was collected</option> <option value="specimen_voucher">identifier for the sample culture including institute and collection code</option> <option value="altitude">Altitude (m)</option> <option value="dev_stage">sample obtained from an organism in a specific developmental stage</option> <option value="isolate">individual isolate from which sample was obtained</option> <option value="location">geographic location of isolation of the sample</option> <option value="study_accession">study accession number</option> <option value="germline">the sample is an unrearranged molecule that was inherited from the parental germline</option> <option value="description">brief sequence description</option> <option value="tissue_lib">tissue library from which sample was obtained</option> <option value="isolation_source">describes the physical, environmental and/or local geographical source of the sample</option> <option value="mating_type">mating type of the organism from which the sequence was obtained</option> <option value="serovar">serological variety of a species (usually a prokaryote) characterized by its antigenic properties</option> <option value="serotype">serological variety of a species characterized by its antigenic properties</option> <option value="sub_strain">name or identifier of a genetically or otherwise modified strain from which sample was obtained</option> <option value="cultivar">cultivar (cultivated variety) of plant from which sample was obtained</option> <option value="collected_by">name of the person who collected the specimen</option> <option value="sub_species">name of sub-species of organism from which sample was obtained</option> <option value="first_public">date when made public</option> <option value="strain">strain from which sample was obtained</option> <option value="country">locality of sample isolation: country names, oceans or seas, followed by regions and localities</option> <option value="variety">variety (varietas, a formal Linnaean rank) of organism from which sample was derived</option> <option value="environmental_sample">identifies sequences derived by direct molecular isolation from an environmental DNA sample</option> <option value="tissue_type">tissue type from which the sample was obtained</option> <option value="keywords">keywords associated with sequence</option> <option value="culture_collection">identifier for the sample culture including institute and collection code</option> </param> </when> <when value="fasta"/> </conditional> </when> <when value="analysis_study"> <repeat name="queries" title="Add a query"> <param name="combination_operation" type="select" label="Combination operation"> <option value="AND">AND</option> <option value="OR">OR</option> <option value="NOT">NOT</option> </param> <conditional name="filter_field"> <param name="field" type="select" label="Field to query"> <option value="study_title">brief sequencing study description</option> <option value="secondary_study_accession">project accession number</option> <option value="study_alias">submitter's name for the study</option> <option value="study_accession">study accession number</option> </param> <when value="study_title"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="secondary_study_accession"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="study_alias"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="study_accession"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> </conditional> </repeat> <conditional name="display_opt"> <param argument="--display" type="select" label="Display option to specify the display format"> <expand macro="display_options"/> </param> <when value="xml"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> </when> <when value="text"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> </when> <when value="fastq"/> <when value="html"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> </when> <when value="report"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> <param argument="--fields" type="select" multiple="true" label="Fields to return"> <option value="study_accession">study_accession</option> <option value="secondary_study_accession">secondary_study_accession</option> <option value="study_title">study_title</option> <option value="study_alias">study_alias</option> </param> <param argument="--sortfields" type="select" optional="true" multiple="true" label="Fields to sort the results"> <option value="study_title">brief sequencing study description</option> <option value="secondary_study_accession">project accession number</option> <option value="study_alias">submitter's name for the study</option> <option value="study_accession">study accession number</option> </param> </when> <when value="fasta"/> </conditional> </when> <when value="noncoding_update"> <repeat name="queries" title="Add a query"> <param name="combination_operation" type="select" label="Combination operation"> <option value="AND">AND</option> <option value="OR">OR</option> <option value="NOT">NOT</option> </param> <conditional name="filter_field"> <param name="field" type="select" label="Field to query"> <option value="mol_type">in vivo molecule type of the sequence</option> <option value="last_updated">date when last updated</option> <option value="sequence_md5"></option> <option value="collected_by">name of the person who collected the specimen</option> <option value="serotype">serological variety of a species characterized by its antigenic properties</option> <option value="sex">sex of the organism from which the sample was obtained</option> <option value="keywords">keywords associated with sequence</option> <option value="cell_line">cell line from which the sample was obtained</option> <option value="inference">a structured description of non-experimental evidence</option> <option value="bio_material">identifier for biological material including institute and collection code</option> <option value="identified_by">name of the taxonomist who identified the specimen</option> <option value="note">any comment or additional information</option> <option value="locus_tag">a submitter-supplied, systematic, stable identifier for a gene and its associated features</option> <option value="lab_host">scientific name of the laboratory host used to propagate the source organism for the sample</option> <option value="tax_division">taxonomic division</option> <option value="collection_date">date that the specimen was collected</option> <option value="specimen_voucher">identifier for the sample culture including institute and collection code</option> <option value="dev_stage">sample obtained from an organism in a specific developmental stage</option> <option value="isolate">individual isolate from which sample was obtained</option> <option value="anticodon">location of the anticodon of tRNA and the amino acid for which it codes</option> <option value="experiment">a brief description of the nature of the experimental evidence</option> <option value="location">geographic location of isolation of the sample</option> <option value="study_accession">study accession number</option> <option value="function">function attributed to a sequence</option> <option value="germline">the sample is an unrearranged molecule that was inherited from the parental germline</option> <option value="product">name of the product associated with the feature</option> <option value="description">brief sequence description</option> <option value="ecotype">a population within a given species displaying traits that reflect adaptation to a local habitat</option> <option value="cell_type">cell type from which the sample was obtained</option> <option value="accession">accession number</option> <option value="isolation_source">describes the physical, environmental and/or local geographical source of the sample</option> <option value="mating_type">mating type of the organism from which the sequence was obtained</option> <option value="tissue_type">tissue type from which the sample was obtained</option> <option value="sub_strain">name or identifier of a genetically or otherwise modified strain from which sample was obtained</option> <option value="tissue_lib">tissue library from which sample was obtained</option> <option value="cultivar">cultivar (cultivated variety) of plant from which sample was obtained</option> <option value="base_count">number of base pairs</option> <option value="topology">sequence topology: circular or linear</option> <option value="sub_species">name of sub-species of organism from which sample was obtained</option> <option value="environmental_sample">identifies sequences derived by direct molecular isolation from an environmental DNA sample</option> <option value="first_public">date when made public</option> <option value="strain">strain from which sample was obtained</option> <option value="country">locality of sample isolation: country names, oceans or seas, followed by regions and localities</option> <option value="variety">variety (varietas, a formal Linnaean rank) of organism from which sample was derived</option> <option value="host">natural (as opposed to laboratory) host to the organism from which sample was obtained</option> <option value="gene_synonym">synonymous, replaced, obsolete or former gene symbol</option> <option value="organelle">membrane-bound intracellular structure from which the sequence was obtained</option> <option value="serovar">serological variety of a species (usually a prokaryote) characterized by its antigenic properties</option> <option value="rna_class">classification of RNA</option> <option value="dataclass">sequence data class</option> <option value="gene">symbol of the gene corresponding to a sequence region</option> <option value="culture_collection">identifier for the sample culture including institute and collection code</option> </param> <when value="mol_type"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/> </when> <when value="last_updated"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> <option value="lower">lower</option> <option value="equal or lower">equal or lower</option> <option value="higher">higher</option> <option value="equal or higher">equal or higher</option> </param> <param name="value" type="text" value="" label="A date in the format YYYY-MM-DD"/> </when> <when value="sequence_md5"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="collected_by"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="serotype"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="sex"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/> </when> <when value="keywords"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="cell_line"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="inference"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="bio_material"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="identified_by"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="note"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="locus_tag"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="lab_host"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="tax_division"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/> </when> <when value="collection_date"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> <option value="lower">lower</option> <option value="equal or lower">equal or lower</option> <option value="higher">higher</option> <option value="equal or higher">equal or higher</option> </param> <param name="value" type="text" value="" label="A date in the format YYYY-MM-DD"/> </when> <when value="specimen_voucher"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="dev_stage"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="isolate"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="anticodon"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="experiment"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="location"> <conditional name="op"> <param name="operation" type="select" label="Operation"> <option value="geo_box2">All locations within a box defined by a centre point and a radius in km.</option> <option value="geo_box1">All locations within a box defined by the lower left (SW) and upper right (NE) points.</option> <option value="geo_circ">All locations within a circle defined by a centre point and a radius in km.</option> <option value="geo_lat">All locations within a latitude range given by a latitude and a radius in km.</option> <option value="geo_south">All locations south of a given latitude (inclusive).</option> <option value="geo_point">An exact lat/lon position</option> <option value="geo_north">All locations north of a given latitude (inclusive).</option> </param> <when value="geo_box2"> <param name="values" type="text" value="" label="latitude, longitude, radius (km)" help="Values separated by simple comma"/> </when> <when value="geo_box1"> <param name="values" type="text" value="" label="south-west latitude, south-west longitude, north-east latitude, north-east longitude" help="Values separated by simple comma"/> </when> <when value="geo_circ"> <param name="values" type="text" value="" label="latitude, longitude, radius (km)" help="Values separated by simple comma"/> </when> <when value="geo_lat"> <param name="values" type="text" value="" label="latitude, radius (km)" help="Values separated by simple comma"/> </when> <when value="geo_south"> <param name="values" type="text" value="" label="latitude" help="Values separated by simple comma"/> </when> <when value="geo_point"> <param name="values" type="text" value="" label="latitude, longitude" help="Values separated by simple comma"/> </when> <when value="geo_north"> <param name="values" type="text" value="" label="latitude" help="Values separated by simple comma"/> </when> </conditional> </when> <when value="study_accession"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="function"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="germline"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> </param> <param name="value" type="select" label="Value"> <option value="yes">yes</option> <option value="true">true</option> <option value="no">no</option> <option value="false">false</option> </param> </when> <when value="product"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="description"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="ecotype"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="cell_type"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="accession"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="isolation_source"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="mating_type"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="tissue_type"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="sub_strain"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="tissue_lib"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="cultivar"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="base_count"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> <option value="lower">lower</option> <option value="equal or lower">equal or lower</option> <option value="higher">higher</option> <option value="equal or higher">equal or higher</option> </param> <param name="value" type="float" value="" label="Any integer"/> </when> <when value="topology"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/> </when> <when value="sub_species"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="environmental_sample"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> </param> <param name="value" type="select" label="Value"> <option value="yes">yes</option> <option value="true">true</option> <option value="no">no</option> <option value="false">false</option> </param> </when> <when value="first_public"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> <option value="lower">lower</option> <option value="equal or lower">equal or lower</option> <option value="higher">higher</option> <option value="equal or higher">equal or higher</option> </param> <param name="value" type="text" value="" label="A date in the format YYYY-MM-DD"/> </when> <when value="strain"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="country"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="variety"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="host"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="gene_synonym"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="organelle"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/> </when> <when value="serovar"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="rna_class"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/> </when> <when value="dataclass"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="A text value from the controlled vocabulary enclosed in double quotes"/> </when> <when value="gene"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> <when value="culture_collection"> <param name="operation" type="select" label="Operator"> <option value="equal">equal</option> <option value="different">different</option> </param> <param name="value" type="text" value="" label="Any text value enclosed in double quotes. Wildcard (*) can be used at the start and/or end of the text value."/> </when> </conditional> </repeat> <conditional name="display_opt"> <param argument="--display" type="select" label="Display option to specify the display format"> <expand macro="display_options"/> </param> <when value="xml"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> </when> <when value="text"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> </when> <when value="fastq"/> <when value="html"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> </when> <when value="report"> <param argument="--offset" type="integer" optional="true" label="First record to get"/> <param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/> <param argument="--fields" type="select" multiple="true" label="Fields to return"> <option value="accession">accession</option> <option value="base_count">base_count</option> <option value="collected_by">collected_by</option> <option value="dataclass">dataclass</option> <option value="first_public">first_public</option> <option value="last_updated">last_updated</option> <option value="location">location</option> <option value="tax_division">tax_division</option> <option value="tax_id">tax_id</option> <option value="scientific_name">scientific_name</option> <option value="rna_class">rna_class</option> <option value="gene">gene</option> <option value="gene_synonym">gene_synonym</option> <option value="product">product</option> <option value="anticodon">anticodon</option> <option value="function">function</option> <option value="locus_tag">locus_tag</option> <option value="experiment">experiment</option> <option value="inference">inference</option> <option value="note">note</option> <option value="bio_material">bio_material</option> <option value="cell_line">cell_line</option> <option value="cell_type">cell_type</option> <option value="country">country</option> <option value="cultivar">cultivar</option> <option value="culture_collection">culture_collection</option> <option value="description">description</option> <option value="dev_stage">dev_stage</option> <option value="ecotype">ecotype</option> <option value="environmental_sample">environmental_sample</option> <option value="germline">germline</option> <option value="host">host</option> <option value="identified_by">identified_by</option> <option value="isolate">isolate</option> <option value="isolation_source">isolation_source</option> <option value="keywords">keywords</option> <option value="lab_host">lab_host</option> <option value="mating_type">mating_type</option> <option value="mol_type">mol_type</option> <option value="organelle">organelle</option> <option value="serotype">serotype</option> <option value="serovar">serovar</option> <option value="sex">sex</option> <option value="collection_date">collection_date</option> <option value="submitted_sex">submitted_sex</option> <option value="specimen_voucher">specimen_voucher</option> <option value="strain">strain</option> <option value="sub_species">sub_species</option> <option value="sub_strain">sub_strain</option> <option value="tissue_lib">tissue_lib</option> <option value="tissue_type">tissue_type</option> <option value="topology">topology</option> <option value="variety">variety</option> <option value="sequence_md5">sequence_md5</option> <option value="study_accession">study_accession</option> </param> <param argument="--sortfields" type="select" optional="true" multiple="true" label="Fields to sort the results"> <option value="mol_type">in vivo molecule type of the sequence</option> <option value="last_updated">date when last updated</option> <option value="sequence_md5"></option> <option value="collected_by">name of the person who collected the specimen</option> <option value="serotype">serological variety of a species characterized by its antigenic properties</option> <option value="sex">sex of the organism from which the sample was obtained</option> <option value="keywords">keywords associated with sequence</option> <option value="cell_line">cell line from which the sample was obtained</option> <option value="inference">a structured description of non-experimental evidence</option> <option value="bio_material">identifier for biological material including institute and collection code</option> <option value="identified_by">name of the taxonomist who identified the specimen</option> <option value="note">any comment or additional information</option> <option value="locus_tag">a submitter-supplied, systematic, stable identifier for a gene and its associated features</option> <option value="lab_host">scientific name of the laboratory host used to propagate the source organism for the sample</option> <option value="tax_division">taxonomic division</option> <option value="collection_date">date that the specimen was collected</option> <option value="specimen_voucher">identifier for the sample culture including institute and collection code</option> <option value="dev_stage">sample obtained from an organism in a specific developmental stage</option> <option value="isolate">individual isolate from which sample was obtained</option> <option value="anticodon">location of the anticodon of tRNA and the amino acid for which it codes</option> <option value="experiment">a brief description of the nature of the experimental evidence</option> <option value="location">geographic location of isolation of the sample</option> <option value="study_accession">study accession number</option> <option value="function">function attributed to a sequence</option> <option value="germline">the sample is an unrearranged molecule that was inherited from the parental germline</option> <option value="product">name of the product associated with the feature</option> <option value="description">brief sequence description</option> <option value="ecotype">a population within a given species displaying traits that reflect adaptation to a local habitat</option> <option value="cell_type">cell type from which the sample was obtained</option> <option value="accession">accession number</option> <option value="isolation_source">describes the physical, environmental and/or local geographical source of the sample</option> <option value="mating_type">mating type of the organism from which the sequence was obtained</option> <option value="tissue_type">tissue type from which the sample was obtained</option> <option value="sub_strain">name or identifier of a genetically or otherwise modified strain from which sample was obtained</option> <option value="tissue_lib">tissue library from which sample was obtained</option> <option value="cultivar">cultivar (cultivated variety) of plant from which sample was obtained</option> <option value="base_count">number of base pairs</option> <option value="topology">sequence topology: circular or linear</option> <option value="sub_species">name of sub-species of organism from which sample was obtained</option> <option value="environmental_sample">identifies sequences derived by direct molecular isolation from an environmental DNA sample</option> <option value="first_public">date when made public</option> <option value="strain">strain from which sample was obtained</option> <option value="country">locality of sample isolation: country names, oceans or seas, followed by regions and localities</option> <option value="variety">variety (varietas, a formal Linnaean rank) of organism from which sample was derived</option> <option value="host">natural (as opposed to laboratory) host to the organism from which sample was obtained</option> <option value="gene_synonym">synonymous, replaced, obsolete or former gene symbol</option> <option value="organelle">membrane-bound intracellular structure from which the sequence was obtained</option> <option value="serovar">serological variety of a species (usually a prokaryote) characterized by its antigenic properties</option> <option value="rna_class">classification of RNA</option> <option value="dataclass">sequence data class</option> <option value="gene">symbol of the gene corresponding to a sequence region</option> <option value="culture_collection">identifier for the sample culture including institute and collection code</option> </param> </when> <when value="fasta"/> </conditional> </when> </conditional> </xml> </macros>