Mercurial > repos > iuc > enasearch_search_data
changeset 0:fc42e7901a23 draft
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/enasearch/ commit 6eda25f5cccc0cf9be09c38a8b48d37aff56ed87
| author | iuc |
|---|---|
| date | Tue, 29 Aug 2017 04:13:28 -0400 |
| parents | |
| children | 6e692d5a5599 |
| files | README.md enasearch_search_data.xml generate_macros.py macros.xml search_macros.xml |
| diffstat | 5 files changed, 10026 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.md Tue Aug 29 04:13:28 2017 -0400 @@ -0,0 +1,11 @@ +ENASearch +========= + +[ENASearch](https://github.com/bebatut/enasearch) is a Python library for interacting with [ENA](http://www.ebi.ac.uk/ena/browse/programmatic-access)'s API. + +For any change in the `macros.xml`, please change on [`generate_macros.py`](generate_macros.py) and regenerate the `macros.xml` with + +``` +$ conda install enasearch +$ python generate_macros.py +``` \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/enasearch_search_data.xml Tue Aug 29 04:13:28 2017 -0400 @@ -0,0 +1,143 @@ +<tool id="enasearch_search_data" name="Search ENA data" version="@WRAPPER_VERSION@.0"> + <description>given a query</description> + <macros> + <import>macros.xml</import> + <import>search_macros.xml</import> + </macros> + <expand macro="requirements"/> + <expand macro="version"/> + <command detect_errors="aggressive"><![CDATA[ +enasearch + search_data + $query_type.free_text_search + #if $query_type.free_text_search == '--free_text_search' + --query '$query_type.query' + --result '$query_type.res.result' + @SEARCH_DATA_DISPLAY@ + #else + --result '$query_type.res.result' + #set $queries='' + #set $sep='' + #for $i, $s in enumerate( $query_type.res.queries ) + #if $sep == '' + #set $sep = str($s.combination_operation) + #else + #set $sep = str($s.combination_operation) + #set $queries += ' %s ' % ($sep) + #end if + #if $s.filter_field.field != 'location' + #set $queries += '%s' % (str($s.filter_field.field)) + #if str($s.filter_field.operation) == "equal" + #set $queries += '=' + #elif str($s.filter_field.operation) == "different" + #set $queries += '!=' + #elif str($s.filter_field.operation) == "lower" + #set $queries += '<' + #elif str($s.filter_field.operation) == "equal or lower" + #set $queries += '<=' + #elif str($s.filter_field.operation) == "higher" + #set $queries += '>' + #elif str($s.filter_field.operation) == "equal or higher" + #set $queries += '>=' + #end if + #set $queries += '"%s"' % (str($s.filter_field.value)) + #else + #set $queries += '%s(%s)' % (str($s.filter_field.operation),str($s.filter_field.values)) + #end if + #end for + --query '$queries' + @SEARCH_DATA_DISPLAY@ + #end if + --file '$output' + --download 'txt' + ]]></command> + <inputs> + <conditional name="query_type"> + <param argument="--free_text_search" type="select" label="Use free text search?" help="If not, the ENA data warehouse is used"> + <option value="--free_text_search">Yes</option> + <option value="">False</option> + </param> + <when value="--free_text_search"> + <param argument="--query" type="text" label="Query"/> + <expand macro="free_text_search"/> + </when> + <when value=""> + <expand macro="conditional_text_search"/> + </when> + </conditional> + </inputs> + <outputs> + <data name="output" format="tabular" label="${tool.name}"> + <change_format> + <when input="query_type.res.display_opt.display" value="fasta" format="fasta" /> + <when input="query_type.res.display_opt.display" value="fastq" format="fastq" /> + <when input="query_type.res.display_opt.display" value="html" format="html" /> + <when input="query_type.res.display_opt.display" value="text" format="text" /> + <when input="query_type.res.display_opt.display" value="xml" format="xml" /> + </change_format> + </data> + </outputs> + <tests> + <test> + <conditional name="query_type"> + <param name="free_text_search" value="--free_text_search"/> + <param name="query" value="kinase+homo+sapiens"/> + <conditional name="res"> + <param name="result" value="sequence_update"/> + <conditional name="display_opt"> + <param name="display" value="fasta"/> + </conditional> + </conditional> + </conditional> + <output name="output" ftype="fasta" md5="d02da99308bbf1e432fc5614c1982994"/> + </test> + <test> + <conditional name="query_type"> + <param name="free_text_search" value="--free_text_search"/> + <param name="query" value="kinase+homo+sapiens"/> + <conditional name="res"> + <param name="result" value="wgs_set"/> + <conditional name="display_opt"> + <param name="display" value="report"/> + <param name="fields" value="accession,environmental_sample"/> + </conditional> + </conditional> + </conditional> + <output name="output" ftype="tabular" md5="c1f91a8276f59c90ec53025e1a3d31d5"/> + </test> + <test> + <conditional name="query_type"> + <param name="free_text_search" value=""/> + <conditional name="res"> + <param name="result" value="coding_release"/> + <repeat name="queries"> + <param name="combination_operation" value="AND"/> + <conditional name="filter_field"> + <param name="field" value="dataclass"/> + <param name="operation" value="equal"/> + <param name="value" value="STD"/> + </conditional> + </repeat> + <repeat name="queries"> + <param name="combination_operation" value="AND"/> + <conditional name="filter_field"> + <param name="field" value="tissue_lib"/> + <param name="operation" value="equal"/> + <param name="value" value="lambda gt11"/> + </conditional> + </repeat> + <conditional name="display_opt"> + <param name="display" value="xml"/> + </conditional> + </conditional> + </conditional> + <output name="output" ftype="xml" md5="0ed405b4db2bcaf9c1540307fe15e9bb"/> + </test> + </tests> + <help><![CDATA[ +**What it does** + +This tool retrieve ENA taxon data + ]]></help> + <expand macro="citations"/> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/generate_macros.py Tue Aug 29 04:13:28 2017 -0400 @@ -0,0 +1,227 @@ +#!/usr/bin/env python + +import enasearch + +spaces = ' ' +operator_names = { + "=": "equal", + "!=": "different", + "<": "lower", + "<=": "equal or lower", + ">": "higher", + ">=": "equal or higher", +} + + +def format_name(name, alternative_name): + """ + Format name to remove None name and & in name + """ + if name is None: + name = alternative_name + name = name.replace("&", "and") + return name + + +def sort_by_name(dict): + """ + Sort a dictionary on the values + """ + return sorted(dict, key=dict.get) + + +def write_analysis_fields(): + """ + Write the analysis fields + """ + s = '%s<xml name="analysis_fields">\n' % (spaces) + fields = enasearch.get_returnable_fields(result="analysis", verbose=False) + for f in fields: + s += '%s<option value="%s">%s</option>\n' % (2 * spaces, f, f) + s += '%s</xml>\n' % (spaces) + return s + + +def write_display_options(): + """ + Write the display options + """ + s = '%s<xml name="display_options">\n' % (spaces) + when_s = '%s<xml name="when_display_options">\n' % (spaces) + options = enasearch.get_display_options(verbose=False) + for opt in options: + s += '%s<option value="%s">%s</option>\n' % (2 * spaces, opt, options[opt]['description']) + when_s += '%s<when value="%s">\n' % (2 * spaces, opt) + if opt == 'fasta' or opt == 'fastq': + when_s += '%s<param name="range_start" argument="--subseq_range" type="integer" optional="true" label="Start integer for subsequences"/>\n' % (3 * spaces) + when_s += '%s<param name="range_stop" argument="--subseq_range" type="integer" optional="true" label="Stop integer for subsequences"/>\n' % (3 * spaces) + else: + when_s += '%s<param argument="--offset" type="integer" optional="true" label="First record to get"/>\n' % (3 * spaces) + when_s += '%s<param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>\n' % (3 * spaces) + when_s += '%s</when>\n' % (2 * spaces) + s += '%s</xml>\n' % (spaces) + when_s += '%s</xml>\n' % (spaces) + s += when_s + return s + + +def write_run_fields(): + """ + Write the run fields + """ + s = '%s<xml name="run_fields">\n' % (spaces) + fields = enasearch.get_returnable_fields(result="read_run", verbose=False) + for f in fields: + s += '%s<option value="%s">%s</option>\n' % (2 * spaces, f, f) + s += '%s</xml>\n' % (spaces) + return s + + +def write_taxonomy_results(): + """ + Write the possible taxonomy results + """ + s = '%s<xml name="taxonomy_results">\n' % (spaces) + fields = enasearch.get_taxonomy_results(verbose=False) + for f in fields: + s += '%s<option value="%s">%s</option>\n' % (2 * spaces, f, fields[f]['description']) + s += '%s</xml>\n' % (spaces) + return s + + +def write_result_parameters(fts=False): + """ + Write the parameters that are dependant of results + """ + res = enasearch.get_results(verbose=False) + options = enasearch.get_display_options(verbose=False) + ft = enasearch.get_filter_types(verbose=False) + # Format the filter type related parameters + ft_parameters = {} + for t in ft: + s = '' + if 'operators' in ft[t]: + s = '%s<param name="operation" type="select" label="Operator">\n' % (7 * spaces) + for o in ft[t]['operators']: + on = o + if o in operator_names: + on = operator_names[o] + s += '%s<option value="%s">%s</option>\n' % (8 * spaces, on, on) + s += '%s</param>\n' % (7 * spaces) + if 'value' in ft[t]: + value_format = 'float' if t == 'Number' else 'text' + s += '%s<param name="value" type="%s" value="" label="%s"/>\n' % (7 * spaces, value_format, ft[t]['value']) + elif 'values' in ft[t]: + s += '%s<param name="value" type="select" label="Value">\n' % (7 * spaces) + for v in ft[t]['values']: + s += '%s<option value="%s">%s</option>\n' % (8 * spaces, v, v) + s += '%s</param>\n' % (7 * spaces) + else: + s += '%s<conditional name="op">\n' % (7 * spaces) + s += '%s<param name="operation" type="select" label="Operation">\n' % (8 * spaces) + for op in ft[t]: + s += '%s<option value="%s">%s</option>\n' % (9 * spaces, op, ft[t][op]['description']) + s += '%s</param>\n' % (8 * spaces) + for op in ft[t]: + s += '%s<when value="%s">\n' % (8 * spaces, op) + s += '%s<param name="values" type="text" value="" label="%s" help="Values separated by simple comma"/>\n' % (9 * spaces, ",".join(ft[t][op]['parameters'])) + s += '%s</when>\n' % (8 * spaces) + s += '%s</conditional>\n' % (7 * spaces) + ft_parameters[t] = s + # Start adding the conditional + s = '%s<conditional name="res">\n' % (2 * spaces) + # Add result parameter + s += '%s<param argument="--result" type="select" label="Result to return">\n' % (3 * spaces) + for r in res: + s += '%s<option value="%s">%s</option>\n' % (4 * spaces, r, res[r]['description']) + s += '%s</param>\n' % (3 * spaces) + for r in res: + sf = enasearch.get_sortable_fields(r) + ff = res[r]['filter_fields'] + s += '%s<when value="%s">\n' % (3 * spaces, r) + if not fts: + s += '%s<repeat name="queries" title="Add a query">\n' % (4 * spaces) + # Add combination operator + s += '%s<param name="combination_operation" type="select" label="Combination operation">\n' % (5 * spaces) + s += '%s<option value="AND">AND</option>\n' % (6 * spaces) + s += '%s<option value="OR">OR</option>\n' % (6 * spaces) + s += '%s<option value="NOT">NOT</option>\n' % (6 * spaces) + s += '%s</param>\n' % (5 * spaces) + s += '%s<conditional name="filter_field">\n' % (5 * spaces) + s += '%s<param name="field" type="select" label="Field to query">\n' % (6 * spaces) + for f in ff: + s += '%s<option value="%s">%s</option>\n' % (7 * spaces, f, ff[f]['description']) + s += '%s</param>\n' % (6 * spaces) + for f in ff: + # Add the correct parameter given the type of field + typ = ff[f]['type'].capitalize() + if typ not in ft_parameters: + if f == 'location': + typ = 'Geospatial' + else: + continue + s += '%s<when value="%s">\n' % (6 * spaces, f) + s += ft_parameters[typ] + s += '%s</when>\n' % (6 * spaces) + s += '%s</conditional>\n' % (5 * spaces) + s += '%s</repeat>\n' % (4 * spaces) + # Add display opt + s += '%s<conditional name="display_opt">\n' % (4 * spaces) + s += '%s<param argument="--display" type="select" label="Display option to specify the display format">\n' % (5 * spaces) + s += '%s<expand macro="display_options"/>\n' % (6 * spaces) + s += '%s</param>\n' % (5 * spaces) + for opt in options: + s += '%s<when value="%s"' % (5 * spaces, opt) + if opt != 'fasta' and opt != 'fastq': + s += '>\n' + s += '%s<param argument="--offset" type="integer" optional="true" label="First record to get"/>\n' % (6 * spaces) + s += '%s<param argument="--length" type="integer" optional="true" label="Number of records to retrieve"/>\n' % (6 * spaces) + if opt == 'report': + s += '%s<param argument="--fields" type="select" multiple="true" label="Fields to return">\n' % (6 * spaces) + for f in res[r]['returnable_fields']: + s += '%s<option value="%s">%s</option>\n' % (7 * spaces, f, f) + s += '%s</param>\n' % (6 * spaces) + s += '%s<param argument="--sortfields" type="select" optional="true" multiple="true" label="Fields to sort the results">\n' % (6 * spaces) + for f in sf: + s += '%s<option value="%s">%s</option>\n' % (7 * spaces, f, sf[f]['description']) + s += '%s</param>\n' % (6 * spaces) + s += '%s</when>\n' % (5 * spaces) + else: + s += '/>\n' + s += '%s</conditional>\n' % (4 * spaces) + s += '%s</when>\n' % (3 * spaces) + s += '%s</conditional>\n' % (2 * spaces) + return s + + +def write_search_data_parameters(): + """ + Write the parameters for search_data + """ + fts = '%s<xml name="free_text_search">\n' % (spaces) + fts += write_result_parameters(True) + fts += '%s</xml>\n' % (spaces) + cts = '%s<xml name="conditional_text_search">\n' % (spaces) + cts += write_result_parameters(False) + cts += '%s</xml>\n' % (spaces) + return fts + cts + + +def generate_search_macros(filepath): + """ + Generate the content of the macro file + """ + s = '<?xml version="1.0" ?>\n' + s += '<macros>\n' + s += write_analysis_fields() + s += write_display_options() + s += write_run_fields() + s += write_taxonomy_results() + s += write_search_data_parameters() + s += '</macros>\n' + with open(filepath, "w") as file: + file.write(s) + + +if __name__ == '__main__': + generate_search_macros("search_macros.xml")
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Tue Aug 29 04:13:28 2017 -0400 @@ -0,0 +1,96 @@ +<?xml version="1.0" ?> +<macros> + <token name="@WRAPPER_VERSION@">0.1.1</token> + <xml name="version"> + <version_command>@WRAPPER_VERSION@</version_command> + </xml> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@WRAPPER_VERSION@">enasearch</requirement> + <yield/> + </requirements> + </xml> + <xml name="citations"/> + <token name="@IDS@"> +<![CDATA[ + #for $id in str($ids).split(',') + --ids '$id' + #end for +]]> + </token> + <xml name="display_opt"> + <conditional name="display_opt"> + <param argument="--display" type="select" label="Display option to specify the display format"> + <expand macro="display_options"/> + </param> + <expand macro="when_display_options"/> + </conditional> + </xml> + <token name="@DISPLAY@"> +<![CDATA[ + --display '$display_opt.display' + #if $display_opt.display == 'fasta' or $display_opt.display == 'fastq' + #if str($display_opt.range_start) != '' and str($display_opt.range_stop) != '' + --subseq_range '$display_opt.range_start'-'$display_opt.range_stop' + #end if + #else + #if str($display_opt.offset) != '' + --offset '$display_opt.offset' + #end if + #if str($display_opt.length) != '' + --length '$display_opt.length' + #end if + #end if +]]> + </token> + <xml name="expanded"> + <param argument="--expanded" type="boolean" truevalue="--expanded" falsevalue="" label="Expand a CON record?"/> + </xml> + <xml name="header"> + <param argument="--header" type="boolean" truevalue="--header" falsevalue="" label="Obtain only the header of a record?"/> + </xml> + <xml name="accession"> + <param argument="--accession" type="text" label="Accession id" help="Study accessions (ERP, SRP, DRP, PRJ prefixes), experiment accessions (ERX, SRX, DRX prefixes), sample accessions (ERS, SRS, DRS, SAM prefixes) and run accessions"/> + </xml> + <token name="@FIELDS@"> +<![CDATA[ + #if $fields + #for $f in str($fields).split(',') + --fields '$f' + #end for + #end if +]]> + </token> + <xml name="change_format"> + <change_format> + <when input="display_opt.display" value="fasta" format="fasta" /> + <when input="display_opt.display" value="fastq" format="fastq" /> + <when input="display_opt.display" value="html" format="html" /> + <when input="display_opt.display" value="text" format="text" /> + <when input="display_opt.display" value="xml" format="xml" /> + </change_format> + </xml> + <token name="@SEARCH_DATA_DISPLAY@"> +<![CDATA[ + --display '$query_type.res.display_opt.display' + #if $query_type.res.display_opt.display != 'fasta' and $query_type.res.display_opt.display != 'fastq' + #if str($query_type.res.display_opt.offset) != '' + --offset '$query_type.res.display_opt.offset' + #end if + #if str($query_type.res.display_opt.length) != '' + --length '$query_type.res.display_opt.length' + #end if + #if $query_type.res.display_opt.display == 'report' + #for $f in str($query_type.res.display_opt.fields).split(',') + --fields '$f' + #end for + #if $query_type.res.display_opt.sortfields + #for $f in str($query_type.res.display_opt.sortfields).split(',') + --sortfields '$f' + #end for + #end if + #end if + #end if +]]> + </token> +</macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/search_macros.xml Tue Aug 29 04:13:28 2017 -0400 @@ -0,0 +1,9549 @@ +<?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>