Mercurial > repos > iuc > ebi_metagenomics_run_downloader
changeset 0:e2e9fae080ad draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ebi_tools commit 7a9c88c1c80b80aaa63e55e9d9125b6a4dd695ac
| author | iuc |
|---|---|
| date | Thu, 01 Dec 2016 15:27:59 -0500 |
| parents | |
| children | d4e7e110dfdb |
| files | README.md download_ebi_metagenomics_run_data ebeye_urllib.py ebi_metagenomics_run_downloader.xml environment.yml generate_macros.py macros.xml test-data/ERR675640_qc-stats_stats |
| diffstat | 8 files changed, 10074 insertions(+), 0 deletions(-) [+] |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.md Thu Dec 01 15:27:59 2016 -0500 @@ -0,0 +1,14 @@ +EBI Search +========== + +EBI Search is a tool to provide text search functionality and uniform access to resources and services hosted at the European Bioinformatics Institute. + +As the possible options in EBI Search are numerous, the `macros.xml` for this wrapper with all options is automatically generated using [`ebeye_urllib3.py`](http://www.ebi.ac.uk/Tools/webservices/download_clients/python/urllib/ebeye_urllib3.py) tool from EBI and a Python script ([`generate_macros.py`](generate_macros.py)). + +For any change in the `macros.xml`, please change on [`generate_macros.py`](generate_macros.py) and regenerate the `macros.xml` with + +``` +$ conda env create -f environment.yml +$ source activate ebeye_urllib +(ebeye_urllib) $ python generate_macros.py +``` \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/download_ebi_metagenomics_run_data Thu Dec 01 15:27:59 2016 -0500 @@ -0,0 +1,44 @@ +#!/usr/bin/env bash +set -e + +python_script=$1 +run_id=$2 +information_type=$3 +information_to_download=$4 +chunk_type=$5 +output_file=$6 + +touch $output_file + +run_link=$(python $python_script getRunLink $run_id) +run_link="$run_link/$information_type/$information_to_download" + +if [[ $chunk_type == 'multiple_chunks' ]]; then + chunk_nb=$(curl "$run_link/chunks") + + if [[ "$chunk_nb" < 1 ]]; then + >&2 echo "-----" + >&2 echo "ERROR" + >&2 echo "-----" + >&2 echo "No data are found for this link:" + >&2 echo "$run_link/chunks" + >&2 echo "-----" + exit 6 + fi + + for i in $(seq "$chunk_nb"); do + curl "$run_link/chunks/$i" | gunzip >> $output_file + done +else + curl "$run_link" >> $output_file +fi + +if [ ! -s $output_file ]; then + >&2 echo "-----" + >&2 echo "ERROR" + >&2 echo "-----" + >&2 echo "The output file is empty probably because the following link is not working:" + >&2 echo "$run_link" + >&2 echo "-----" + exit 6 +fi
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ebeye_urllib.py Thu Dec 01 15:27:59 2016 -0500 @@ -0,0 +1,321 @@ +#!/usr/bin/env python +# ====================================================================== +# Script derived from the EB-eye (REST) Python client available at +# http://www.ebi.ac.uk/Tools/webservices/services/eb-eye_rest +# and distributed under the Apache License +# ====================================================================== +# Load libraries +import platform +import os +import urllib +import re +from optparse import OptionParser +from gzip import GzipFile +from xmltramp2 import xmltramp +# python2 +from StringIO import StringIO +import urllib2 +# python3 +# import urllib.request as urllib2 + + +# Service base URL +baseUrl = 'http://www.ebi.ac.uk/ebisearch/ws/rest' + +# Debug level +debugLevel = 0 + + +# Debug print +def printDebugMessage(functionName, message, level): + if(level <= debugLevel): + print ('[' + functionName + '] ' + message) + + +# User-agent for request. +def getUserAgent(): + printDebugMessage('getUserAgent', 'Begin', 11) + urllib_agent = 'Python-urllib/%s' % urllib2.__version__ + clientRevision = '$Revision: 2468 $' + clientVersion = '0' + if len(clientRevision) > 11: + clientVersion = clientRevision[11:-2] + user_agent = 'EBI-Sample-Client/%s (%s; Python %s; %s) %s' % ( + clientVersion, os.path.basename(__file__), + platform.python_version(), platform.system(), + urllib_agent + ) + printDebugMessage('getUserAgent', 'user_agent: ' + user_agent, 12) + printDebugMessage('getUserAgent', 'End', 11) + return user_agent + + +# Wrapper for a REST (HTTP GET) request +def restRequest(url): + printDebugMessage('restRequest', 'Begin', 11) + printDebugMessage('restRequest', 'url: ' + url, 11) + # python 2 + url = urllib.quote(url, safe="%/:=&?~#+!$,;'@()*[]") + # python 3 + # url = urllib.request.quote(url, safe="%/:=&?~#+!$,;'@()*[]") + + try: + user_agent = getUserAgent() + http_headers = { + 'User-Agent': user_agent, + 'Accept-Encoding': 'gzip' + } + req = urllib2.Request(url, None, http_headers) + resp = urllib2.urlopen(req) + # python2 + encoding = resp.info().getheader('Content-Encoding') + # python3 + # encoding = resp.info().__getitem__('Content-Encoding') + result = None + if encoding is None or encoding == 'identity': + # python2 + result = resp.read() + # python3 + # result = str(resp.read(), 'utf-8') + elif encoding == 'gzip': + result = resp.read() + printDebugMessage('restRequest', 'result: ' + str(result), 21) + # python2 + gz = GzipFile( + fileobj=StringIO(result), + mode="r") + result = gz.read() + # python3 + # result = str(gzip.decompress(result), 'utf-8') + else: + raise Exception('Unsupported Content-Encoding') + resp.close() + except urllib2.HTTPError as ex: + raise ex + printDebugMessage('restRequest', 'result: ' + result, 11) + printDebugMessage('restRequest', 'End', 11) + return result + + +def hasSubdomains(domainInfo): + for dir in domainInfo._dir: + if dir._name == 'subdomains': + return True + return False + + +def extractUsefulFields(fieldInfos): + searchable = [] + retrievable = [] + + for fieldInfo in fieldInfos: + if fieldInfo('id') == "$facets": + continue + + options = fieldInfo['options']['option':] + for option in options: + if option("name") == "searchable" and str(option) == "true": + searchable.append(fieldInfo('id')) + if option("name") == "retrievable" and str(option) == "true": + retrievable.append(fieldInfo('id')) + return searchable, retrievable + + +def extractLowerLevelDomains(domainInfo, domains): + if hasSubdomains(domainInfo): + subdomains = domainInfo['subdomains']['domain':] + for subdomain in subdomains: + domains = extractLowerLevelDomains( subdomain, domains) + else: + searchable, retrievable = extractUsefulFields( + domainInfo['fieldInfos']['fieldInfo':]) + + domain_id = domainInfo('id') + domains.setdefault(domain_id, {}) + domains[domain_id]["name"] = domainInfo('name') + domains[domain_id]["searchable_fields"] = sorted(searchable) + domains[domain_id]["retrievable_fields"] = sorted(retrievable) + return domains + + +# Get domain Hierarchy +def getDomainHierarchy(): + requestUrl = baseUrl + '/allebi' + xmlDoc = restRequest(requestUrl) + doc = xmltramp.parse(xmlDoc) + allebi = doc['domains']['domain'] + lower_level_domains = extractLowerLevelDomains(allebi, {}) + printDebugMessage('getDomainHierarchy', 'End', 1) + return lower_level_domains + + +# Check if a databaseInfo matches a database name. +def is_database(dbInfo, dbName): + printDebugMessage('is_database', 'Begin', 11) + retVal = False + if str(dbInfo.name) == dbName: + retVal = True + else: + for dbAlias in dbInfo.aliasList: + if str(dbAlias) == dbName: + retVal = True + printDebugMessage('is_database', 'retVal: ' + str(retVal), 11) + printDebugMessage('is_database', 'End', 11) + return retVal + + +# Get number of results +def getNumberOfResults(domain, query): + printDebugMessage('getNumberOfResults', 'Begin', 1) + requestUrl = baseUrl + '/' + domain + '?query=' + query + '&size=0' + printDebugMessage('getNumberOfResults', requestUrl, 2) + xmlDoc = restRequest(requestUrl) + doc = xmltramp.parse(xmlDoc) + numberOfResults = int(str(doc['hitCount'])) + printDebugMessage('getNumberOfResults', 'End', 1) + return numberOfResults + + +def makeRequest(requestUrl): + xmlDoc = restRequest(requestUrl) + doc = xmltramp.parse(xmlDoc) + entries = doc['entries']['entry':] + formatted_output = printEntries(entries) + return formatted_output + + +# Get search results +def getResults(domain, query, fields): + numberOfResults = getNumberOfResults(domain, query) + maximum_size = 100 + quotient = numberOfResults / maximum_size + start = 0 + + printDebugMessage('getResults', 'Begin', 1) + request_output = "%s\tlink\n" % (fields.replace(",", "\t")) + for i in range(quotient): + start = maximum_size * i + requestUrl = baseUrl + '/' + domain + '?query=' + query + requestUrl += '&fields=' + fields + '&size=' + str(maximum_size) + requestUrl += '&start=' + str(start) + '&fieldurl=true' + request_output += makeRequest(requestUrl) + + if (numberOfResults % 100) > 0: + start = maximum_size * quotient + remainder = numberOfResults - start + requestUrl = baseUrl + '/' + domain + '?query=' + query + requestUrl += '&fields=' + fields + '&size=' + str(remainder) + requestUrl += '&start=' + str(start) + '&fieldurl=true' + request_output += makeRequest(requestUrl) + + print(request_output) + + +def printEntries(entries): + output = "" + printDebugMessage('printEntries', 'Begin', 1) + for entry in entries: + sep = "" + for field in entry['fields']['field':]: + output += "%s" % (sep) + fields = field['values']['value':] + if len(fields) > 0: + sub_sep = "" + for value in field['values']['value':]: + output += "%s%s" % (sub_sep, value) + sub_sep = "," + sep = "\t" + + if hasFieldUrls(entry): + output += "%s" % (sep) + sub_sep = "" + for fieldurl in entry['fieldURLs']['fieldURL':]: + output += "%s%s" % (sub_sep, str(fieldurl)) + sub_sep = "," + sep = "\t" + if hasViewUrls(entry): + output += "%s" % (sep) + sub_sep = "" + for viewurl in entry['viewURLs']['viewURL':]: + output += "%s%s" % (sub_sep, str(viewurl)) + sub_sep = "," + output += "\n" + printDebugMessage('printEntries', 'End', 1) + return output + + +def hasFieldUrls(entry): + for dir in entry._dir: + if dir._name == 'fieldURLs': + return True + return False + + +def hasViewUrls(entry): + for dir in entry._dir: + if dir._name == 'viewURLs': + return True + return False + + +def getRunLink(run_id): + printDebugMessage('getEntries', 'Begin', 1) + requestUrl = baseUrl + '/metagenomics_runs/entry/' + run_id + '?fieldurl=true' + printDebugMessage('getEntries', requestUrl, 2) + xmlDoc = restRequest(requestUrl) + doc = xmltramp.parse(xmlDoc) + entries = doc['entries']['entry':] + fieldURL = '' + for entry in entries: + for fieldurl in entry['fieldURLs']['fieldURL':]: + fieldURL += str(fieldurl) + printDebugMessage('getEntries', 'End', 1) + p = re.compile('http') + fieldURL = p.sub('https', fieldURL) + print fieldURL + + +if __name__ == '__main__': + # Usage message + usage = """ + %prog getDomainHierarchy + %prog getResults <domain> <query> <fields> + %prog getRunLink <runId> + """ + + description = "Tools to query and download data from several EMBL-EBI databases" + description += "The searching tools are using the EB-eye search engine. " + description += "http://www.ebi.ac.uk/ebisearch/" + # Process command-line options + parser = OptionParser( + usage=usage, + description=description, + version='1.0') + (options, args) = parser.parse_args() + + # No arguments, print usage + if len(args) < 1: + parser.print_help() + + # Get domain hierarchy + elif args[0] == 'getDomainHierarchy': + getDomainHierarchy() + + # Get search results + elif args[0] == 'getResults': + if len(args) < 4: + print ('domain, query and fields should be given.') + else: + getResults(args[1], args[2], args[3]) + + # Get run link results + elif args[0] == 'getRunLink': + if len(args) < 2: + print ('run id should be given.') + else: + getRunLink(args[1]) + + # Unknown argument combination, display usage + else: + print ('Error: unrecognised argument combination') + parser.print_help()
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ebi_metagenomics_run_downloader.xml Thu Dec 01 15:27:59 2016 -0500 @@ -0,0 +1,139 @@ +<tool id="ebi_metagenomics_run_downloader" name="Download run data" version="0.1.0"> + <description>from EBI Metagenomics database</description> + + <macros> + <import>macros.xml</import> + </macros> + + <expand macro="requirements"> + <requirement type="package" version="7.49.0">curl</requirement> + </expand> + + <command detect_errors="exit_code"><![CDATA[ + '$__tool_directory__/download_ebi_metagenomics_run_data' + '$__tool_directory__/ebeye_urllib.py' + '$run_id' + '$information.type' + '$information.to_download' + + #if ( $information.type == 'sequences' and $information.to_download != 'ncRNA-tRNA-FASTA') or ($information.type == 'function' and $information.to_download == 'InterProScan') + 'multiple_chunks' + #else + 'single_chunk' + #end if + + 'output.dat' + ]]></command> + + <inputs> + <param name="run_id" type="text" label="Identifiant of the run in EBI Metagenomics" /> + + <conditional name="information"> + <param name="type" type="select" label="Type of information to download"> + <option value="sequences" selected="true">Sequence data</option> + <option value="qc-stats">Quality control statistics</option> + <option value="taxonomy">Taxonomic analysis</option> + <option value="function">Functional analysis</option> + </param> + + <when value="sequences"> + <param name="to_download" type="select" label="Sequences to download"> + <option value="ProcessedReads" selected="true">Processed nucleotide reads</option> + <option value="ReadsWithPredictedCDS">Processed reads with pCDS</option> + <option value="ReadsWithMatches">Processed reads with annotation</option> + <option value="ReadsWithoutMatches">Processed reads without annotation</option> + <option value="PredictedCDSWithAnnotation">Predicted CDS with annotation</option> + <option value="PredictedCDSWithoutAnnotation">Predicted CDS without annotation</option> + <option value="PredictedORFWithoutAnnotation">Predicted ORF without annotation</option> + <option value="ncRNA-tRNA-FASTA">Predicted tRNAs</option> + </param> + </when> + + <when value="qc-stats"> + <param name="to_download" type="select" label="Quality control statistics to download"> + <option value="summary" selected="true">Number of sequence reads per Quality Control step</option> + <option value="stats">Quality control statistics</option> + <option value="length">Read length distribution</option> + <option value="gc_bin">Read GC distribution</option> + <option value="base">Nucleotide position distribution</option> + </param> + </when> + + <when value="taxonomy"> + <param name="to_download" type="select" label="Taxonomic analysis to download"> + <option value="5S-rRNA-FASTA" selected="true">Reads encoding 5S rRNA</option> + <option value="16S-rRNA-FASTA">Reads encoding 16S rRNA</option> + <option value="23S-rRNA-FASTA">Reads encoding 23S rRNA</option> + <option value="OTU-TSV">OTUs, reads and taxonomic assignments (TSV)</option> + <option value="NewickPrunedTree">Phylogenetic tree</option> + </param> + </when> + + <when value="function"> + <param name="to_download" type="select" label="Functional analysis to download"> + <option value="InterProScan" selected="true">InterPro matches</option> + <option value="GOAnnotations">Complete GO annotation</option> + <option value="GOSlimAnnotations">GO slim annotation</option> + </param> + </when> + </conditional> + </inputs> + + <outputs> + <data name="output_file_fasta" format="fasta" label="${tool.name} for ${run_id}" from_work_dir="output.dat"> + <filter>( information['type'] == 'sequences' or + ( information['type'] == 'taxonomy' and ( information['to_download'] == '5S-rRNA-FASTA' or + information['to_download'] == '16S-rRNA-FASTA' or information['to_download'] == '23S-rRNA-FASTA' ))) + </filter> + </data> + <data name="output_file_tsv" format="tsv" label="${tool.name} for ${run_id}" from_work_dir="output.dat"> + <filter>( information['type'] == 'qc-stats' or + ( information['type'] == 'taxonomy' and information['to_download'] == 'OTU-TSV' ) or + ( information['type'] == 'function' and information['to_download'] == 'InterProScan/chunks/1' )) + </filter> + </data> + <data name="output_file_csv" format="csv" label="${tool.name} for ${run_id}" from_work_dir="output.dat"> + <filter>( information['type'] == 'function' and ( information['to_download'] == 'GOAnnotations' or information['to_download'] == 'GOSlimAnnotations' )) + </filter> + </data> + <data name="output_file_newick" format="newick" label="${tool.name} for ${run_id}" from_work_dir="output.dat"> + <filter>( information['type'] == 'taxonomy' and information['to_download'] == 'NewickPrunedTree') + </filter> + </data> + </outputs> + + <tests> + <test> + <param name="run_id" value="ERR675640" /> + <conditional name="information"> + <param name="type" value="qc-stats" /> + <param name="to_download" value="stats" /> + </conditional> + <output name="output_file_tsv" file="ERR675640_qc-stats_stats" /> + </test> + <test> + <param name="run_id" value="ERR675573" /> + <conditional name="information"> + <param name="type" value="sequences" /> + <param name="to_download" value="PredictedCDSWithAnnotation" /> + </conditional> + <output name="output_file_fasta"> + <assert_contents> + <has_line_matching expression="^>ERR675573.1772-FC81EB0ABXX:7:1101:19215:2564-ATCACGAT-1_1_117_- IPR010690/PF06898/2-34$" /> + <has_line_matching expression="^>ERR675573.6692248-FC81EB0ABXX:7:1202:20007:191300-ATCACGAT-1_1_127_- IPR004089/PF00015/2-41|G3DSA:1.10.287.950/2-41$" /> + <has_line_matching expression="^>ERR675573.21754698-FC81EB0ABXX:7:2208:13328:189792-ATCACGAT-1_1_150_- IPR027414/G3DSA:2.70.98.50/7-45$" /> + </assert_contents> + </output> + </test> + </tests> + + <help><![CDATA[ +**What it does** + +The European Bioinformatics Institute (EMBL-EBI) maintains the world’s most comprehensive range of freely available and up-to-date molecular databases + +This tool download data related to a run in EBI Metagenomics database. + ]]></help> + + <expand macro="citations" /> +</tool> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/environment.yml Thu Dec 01 15:27:59 2016 -0500 @@ -0,0 +1,19 @@ +name: ebeye_urllib +channels: !!python/tuple +- biocore +- bioconda +- defaults +dependencies: +- bioconda::urllib3=1.12=py27_0 +- bioconda::xmltramp2=3.1.1=py27_0 +- openssl=1.0.2j=0 +- pip=9.0.1=py27_0 +- python=2.7.12=1 +- readline=6.2=2 +- setuptools=27.2.0=py27_0 +- six=1.10.0=py27_0 +- sqlite=3.13.0=0 +- tk=8.5.18=0 +- wheel=0.29.0=py27_0 +- zlib=1.2.8=3 +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/generate_macros.py Thu Dec 01 15:27:59 2016 -0500 @@ -0,0 +1,141 @@ +#!/usr/bin/env python3 + +import ebeye_urllib + + +def add_option(value, name, selected=False): + to_write = '<option ' + to_write += 'value="%s"' % (value) + if selected: + to_write += ' selected="true"' + to_write += '>%s' % (name) + to_write += '</option>\n' + return to_write + + +def add_select_parameter(name, label, multiple=False): + to_write = '<param ' + to_write += 'name="%s" ' % (name) + to_write += 'type="select" ' + to_write += 'label="%s" ' % (label) + if multiple: + to_write += 'multiple=\"true\"' + to_write += '>\n' + return to_write + + +def write_macros_file(macros_filepath, domains_fields): + spaces = ' ' + to_write = '<macros>\n' + + to_write += '%s<xml name="requirements">\n' % (spaces) + to_write += '%s<requirements>\n' % (2 * spaces) + to_write += '%s<requirement type="package" version="3.1.1">xmltramp2</requirement>\n' % (3 * spaces) + to_write += '%s<requirement type="package" version="1.12">urllib3</requirement>\n' % (3 * spaces) + to_write += '%s<yield/>\n' % (3 * spaces) + to_write += '%s</requirements>\n' % (2 * spaces) + to_write += '%s</xml>\n' % (spaces) + + to_write += '%s<xml name="inputs">\n' % (spaces) + + to_write += '%s<conditional name="searched_domain">\n' % (2 * spaces) + to_write += '%s%s' % (3 * spaces, add_select_parameter( + 'domain', + 'Domain to query')) + + sorted_domains = [(d, domains_fields[d]['name']) for d in domains_fields.keys()] + sorted_domains = sorted(sorted_domains, key=lambda tup: tup[1]) + for domain in sorted_domains: + to_write += '%s%s' % (4 * spaces, add_option( + domain[0], + domain[1])) + + to_write += '%s</param>\n\n' % (3 * spaces) + + for d in sorted_domains: + domain = d[0] + to_write += '%s<when value="%s">\n' % (3 * spaces, domain) + + to_write += '%s%s' % (4 * spaces, add_select_parameter( + 'fields', + 'Fields to extract', + multiple=True)) + for field in domains_fields[domain]['retrievable_fields']: + to_write += '%s%s' % (5 * spaces, add_option( + field, + field, + selected=True)) + to_write += '%s<validator type="no_options" message="Please select at least one field" />\n' % (5 * spaces) + to_write += '%s</param>\n' % (4 * spaces) + + to_write += '%s<repeat name="queries" title="Add a query">\n' % ( + 4 * spaces) + + to_write += '%s%s' % (5 * spaces, add_select_parameter( + 'combination_operation', + 'Combination operation')) + to_write += '%s%s' % (6 * spaces, add_option('AND', 'AND')) + to_write += '%s%s' % (6 * spaces, add_option('OR', 'OR')) + to_write += '%s%s' % (6 * spaces, add_option('NOT', 'NOT')) + to_write += '%s</param>\n' % (5 * spaces) + + to_write += '%s%s' % (5 * spaces, add_select_parameter( + 'query_field', + 'Fields')) + for field in domains_fields[domain]['searchable_fields']: + to_write += '%s%s' % (6 * spaces, add_option(field, field)) + to_write += '%s</param>\n' % (5 * spaces) + + to_write += '%s<conditional name="comp_operation">\n' % (5 * spaces) + to_write += '%s%s' % (6 * spaces, add_select_parameter( + 'operation', + 'Comparison operation')) + to_write += '%s%s' % (7 * spaces, add_option('equal', 'equal')) + to_write += '%s%s' % (7 * spaces, add_option('not', 'not')) + to_write += '%s%s' % (7 * spaces, add_option('range', 'range')) + to_write += '%s</param>\n' % (6 * spaces) + + to_write += '%s<when value="equal">\n' % (6 * spaces) + to_write += '%s<param name="query_text" type="text" label="Searched term"/>\n' % (7 * spaces) + to_write += '%s</when>\n' % (6 * spaces) + + to_write += '%s<when value="not">\n' % (6 * spaces) + to_write += '%s<param name="query_text" type="text" label="Searched term"/>\n' % (7 * spaces) + to_write += '%s<param name="not_query_text" type="text" label="Limiting term"/>\n' % (7 * spaces) + to_write += '%s</when>\n' % (6 * spaces) + + to_write += '%s<when value="range">\n' % (6 * spaces) + to_write += '%s<param name="min" type="text" label="From"/>\n' % (7 * spaces) + to_write += '%s<param name="max" type="text" label="To"/>\n' % ( + 7 * spaces) + to_write += '%s</when>\n' % (6 * spaces) + + to_write += '%s</conditional>\n' % (5 * spaces) + + to_write += '%s</repeat>\n' % (4 * spaces) + + to_write += '%s</when>\n\n' % (3 * spaces) + + to_write += '%s</conditional>\n' % (2 * spaces) + to_write += '%s</xml>\n' % (spaces) + + to_write += '%s<xml name="citations">\n' % (spaces) + to_write += '%s<citations>\n' % (2 * spaces) + to_write += '%s<citation type="doi">10.1093/bib/bbp065</citation>\n' % (3 * spaces) + to_write += '%s<citation type="doi">10.1093/nar/gkv316</citation>\n' % (3 * spaces) + to_write += '%s</citations>\n' % (2 * spaces) + to_write += '%s</xml>\n' % (spaces) + + to_write += '</macros>\n' + + with open(macros_filepath, 'w') as macros_file: + macros_file.write(to_write) + + +def generate_macros(): + domains_fields = ebeye_urllib.getDomainHierarchy() + write_macros_file('macros.xml', domains_fields) + + +if __name__ == '__main__': + generate_macros()
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Thu Dec 01 15:27:59 2016 -0500 @@ -0,0 +1,9383 @@ +<macros> + <xml name="requirements"> + <requirements> + <requirement type="package" version="3.1.1">xmltramp2</requirement> + <requirement type="package" version="1.12">urllib3</requirement> + <yield/> + </requirements> + </xml> + <xml name="inputs"> + <conditional name="searched_domain"> + <param name="domain" type="select" label="Domain to query" > + <option value="sra-analysis">Analysis</option> + <option value="arrayexpress-repository">ArrayExpress</option> + <option value="genome_assembly">Assembly</option> + <option value="wgs_masters">Assembly contig set</option> + <option value="emblrelease_con">Assembly scaffold (Release)</option> + <option value="emblnew_con">Assembly scaffold (Update)</option> + <option value="atlas-genes">Baseline Expression Atlas Genes</option> + <option value="biomodels">BioModels</option> + <option value="biosamples">BioSamples</option> + <option value="biosamples-groups">BioSamples groups</option> + <option value="chebi">ChEBI</option> + <option value="chembl-activity">ChEMBL Activity</option> + <option value="chembl-assay">ChEMBL Assay</option> + <option value="chembl-document">ChEMBL Document</option> + <option value="chembl-molecule">ChEMBL Molecule</option> + <option value="chembl-target">ChEMBL Target</option> + <option value="chembl-target_component">ChEMBL Target Component</option> + <option value="coding_release">Coding (Release)</option> + <option value="coding_update">Coding (Update)</option> + <option value="dgva">DGVa</option> + <option value="atlas-genes-differential">Differential Expression Atlas Genes</option> + <option value="efo">EFO</option> + <option value="ega">EGA</option> + <option value="emdb">EMDB</option> + <option value="epo">EPO</option> + <option value="elixir-registry">Elixir registry</option> + <option value="ensembl_gene">Ensembl Gene</option> + <option value="ensemblGenomes_gene">Ensembl Genomes Gene</option> + <option value="ensemblGenomes_genome">Ensembl Genomes Genome</option> + <option value="ensemblGenomes_seqRegion">Ensembl Genomes Sequence Region</option> + <option value="ensemblGenomes_variant">Ensembl Genomes Variant</option> + <option value="enzymeportal">Enzyme Portal</option> + <option value="enzymeportal_enzymes">Enzyme Portal - Enzymes</option> + <option value="atlas-experiments">Expression Atlas Experiments</option> + <option value="gnps">GNPS</option> + <option value="go">GO</option> + <option value="gpcrdb">GPCRDB</option> + <option value="gpmdb">GPMdb</option> + <option value="hgnc">HGNC</option> + <option value="human_diseases">Human diseases</option> + <option value="imgt-hla">IMGT/HLA</option> + <option value="ipd-kir">IPD-KIR</option> + <option value="ipd-mhc">IPD-MHC</option> + <option value="intact-complexes">IntAct Complexes</option> + <option value="intact-experiments">IntAct Experiments</option> + <option value="intact-interactions">IntAct Interactions</option> + <option value="intact-interactors">IntAct Interactors</option> + <option value="intenz">IntEnz</option> + <option value="interpro">InterPro</option> + <option value="iprmatches">Iprmatches</option> + <option value="jpo">JPO</option> + <option value="kipo">KIPO</option> + <option value="lrg">LRG</option> + <option value="large-assembly">Large assembly</option> + <option value="pdbechem">Ligands</option> + <option value="medline">MEDLINE</option> + <option value="merops_clan">MEROPS Peptidase Clans</option> + <option value="merops_family">MEROPS Peptidase Families</option> + <option value="merops_id">MEROPS Peptidases</option> + <option value="mesh">MESH</option> + <option value="massive">MassIVE</option> + <option value="metabolights">MetaboLights</option> + <option value="metabolights_dataset">MetaboLights Dataset</option> + <option value="metabolome_express">MetabolomeExpress</option> + <option value="metabolomics_workbench">Metabolomics Workbench</option> + <option value="hmmer_hmm">Metadata for HMMER HMM database</option> + <option value="hmmer_seq">Metadata for HMMER sequence database</option> + <option value="metagenomics_projects">Metagenomics Projects</option> + <option value="metagenomics_runs">Metagenomics Runs</option> + <option value="metagenomics_samples">Metagenomics Samples</option> + <option value="nrnl1">NRNL1</option> + <option value="nrnl2">NRNL2</option> + <option value="nrpl1">NRPL1</option> + <option value="nrpl2">NRPL2</option> + <option value="non-coding_release">Non-coding (Release)</option> + <option value="non-coding_update">Non-coding (Update)</option> + <option value="omim">OMIM</option> + <option value="pdbe">PDBe</option> + <option value="pride">PRIDE</option> + <option value="patentFamilies">Patent Families</option> + <option value="patentdb">Patents</option> + <option value="ebiweb_people">People</option> + <option value="peptide_atlas">PeptideAtlas</option> + <option value="pfam">Pfam</option> + <option value="pombase">PomBase</option> + <option value="rnacentral">RNAcentral</option> + <option value="reactome">Reactome</option> + <option value="sra-experiment">Read (Experiment)</option> + <option value="sra-run">Read (Run)</option> + <option value="ebiweb_resources">Resources</option> + <option value="rhea">Rhea</option> + <option value="sbo">SBO</option> + <option value="sra-sample">Sample</option> + <option value="emblrelease_standard">Sequence (Release)</option> + <option value="emblnew_standard">Sequence (Update)</option> + <option value="ebiweb_corporate">Site</option> + <option value="project">Study</option> + <option value="sra-study">Study (Read/Analysis)</option> + <option value="sra-submission">Submission (Read/Analysis)</option> + <option value="taxonomy">Taxonomy</option> + <option value="tsa_masters">Transcriptome assembly contig set</option> + <option value="treefam">TreeFam</option> + <option value="uspto">USPTO</option> + <option value="uniparc">UniParc</option> + <option value="uniprot">UniProtKB</option> + <option value="uniref100">UniRef100</option> + <option value="uniref50">UniRef50</option> + <option value="uniref90">UniRef90</option> + <option value="wormbaseParasite">WormBase ParaSite</option> + </param> + + <when value="sra-analysis"> + <param name="fields" type="select" label="Fields to extract" multiple="true"> + <option value="PROJECT" selected="true">PROJECT</option> + <option value="PUBMED" selected="true">PUBMED</option> + <option value="SRA-STUDY" selected="true">SRA-STUDY</option> + <option value="SRA-SUBMISSION" selected="true">SRA-SUBMISSION</option> + <option value="description" selected="true">description</option> + <option value="domain_source" selected="true">domain_source</option> + <option value="id" selected="true">id</option> + <validator type="no_options" message="Please select at least one field" /> + </param> + <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> + <param name="query_field" type="select" label="Fields" > + <option value="PROJECT">PROJECT</option> + <option value="PUBMED">PUBMED</option> + <option value="SRA-STUDY">SRA-STUDY</option> + <option value="SRA-SUBMISSION">SRA-SUBMISSION</option> + <option value="abstract">abstract</option> + <option value="acc">acc</option> + <option value="alias">alias</option> + <option value="center_name">center_name</option> + <option value="description">description</option> + <option value="domain_source">domain_source</option> + <option value="id">id</option> + </param> + <conditional name="comp_operation"> + <param name="operation" type="select" label="Comparison operation" > + <option value="equal">equal</option> + <option value="not">not</option> + <option value="range">range</option> + </param> + <when value="equal"> + <param name="query_text" type="text" label="Searched term"/> + </when> + <when value="not"> + <param name="query_text" type="text" label="Searched term"/> + <param name="not_query_text" type="text" label="Limiting term"/> + </when> + <when value="range"> + <param name="min" type="text" label="From"/> + <param name="max" type="text" label="To"/> + </when> + </conditional> + </repeat> + </when> + + <when value="arrayexpress-repository"> + <param name="fields" type="select" label="Fields to extract" multiple="true"> + <option value="PUBMED" selected="true">PUBMED</option> + <option value="TAXONOMY" selected="true">TAXONOMY</option> + <option value="data_protocol" selected="true">data_protocol</option> + <option value="description" selected="true">description</option> + <option value="disease" selected="true">disease</option> + <option value="domain_source" selected="true">domain_source</option> + <option value="full_dataset_link" selected="true">full_dataset_link</option> + <option value="id" selected="true">id</option> + <option value="instrument_platform" selected="true">instrument_platform</option> + <option value="name" selected="true">name</option> + <option value="omics_type" selected="true">omics_type</option> + <option value="publication_date" selected="true">publication_date</option> + <option value="sample_protocol" selected="true">sample_protocol</option> + <option value="species" selected="true">species</option> + <option value="submission_date" selected="true">submission_date</option> + <option value="submitter_keywords" selected="true">submitter_keywords</option> + <option value="tissue" selected="true">tissue</option> + <validator type="no_options" message="Please select at least one field" /> + </param> + <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> + <param name="query_field" type="select" label="Fields" > + <option value="PUBMED">PUBMED</option> + <option value="TAXONOMY">TAXONOMY</option> + <option value="acc">acc</option> + <option value="cell_type">cell_type</option> + <option value="data_protocol">data_protocol</option> + <option value="data_synonyms">data_synonyms</option> + <option value="description">description</option> + <option value="description_synonyms">description_synonyms</option> + <option value="disease">disease</option> + <option value="domain_source">domain_source</option> + <option value="full_dataset_link">full_dataset_link</option> + <option value="id">id</option> + <option value="instrument_platform">instrument_platform</option> + <option value="name">name</option> + <option value="name_synonyms">name_synonyms</option> + <option value="omics_type">omics_type</option> + <option value="publication_date">publication_date</option> + <option value="pubmed_abstract">pubmed_abstract</option> + <option value="pubmed_abstract_synonyms">pubmed_abstract_synonyms</option> + <option value="pubmed_authors">pubmed_authors</option> + <option value="pubmed_title">pubmed_title</option> + <option value="pubmed_title_synonyms">pubmed_title_synonyms</option> + <option value="repository">repository</option> + <option value="sample_protocol">sample_protocol</option> + <option value="sample_synonyms">sample_synonyms</option> + <option value="software">software</option> + <option value="species">species</option> + <option value="submission_date">submission_date</option> + <option value="submitter">submitter</option> + <option value="submitter_email">submitter_email</option> + <option value="submitter_keywords">submitter_keywords</option> + <option value="tissue">tissue</option> + <option value="updated_date">updated_date</option> + </param> + <conditional name="comp_operation"> + <param name="operation" type="select" label="Comparison operation" > + <option value="equal">equal</option> + <option value="not">not</option> + <option value="range">range</option> + </param> + <when value="equal"> + <param name="query_text" type="text" label="Searched term"/> + </when> + <when value="not"> + <param name="query_text" type="text" label="Searched term"/> + <param name="not_query_text" type="text" label="Limiting term"/> + </when> + <when value="range"> + <param name="min" type="text" label="From"/> + <param name="max" type="text" label="To"/> + </when> + </conditional> + </repeat> + </when> + + <when value="genome_assembly"> + <param name="fields" type="select" label="Fields to extract" multiple="true"> + <option value="BIOSAMPLE" selected="true">BIOSAMPLE</option> + <option value="PROJECT" selected="true">PROJECT</option> + <option value="SAMPLE" selected="true">SAMPLE</option> + <option value="TAXON" selected="true">TAXON</option> + <option value="description" selected="true">description</option> + <option value="domain_source" selected="true">domain_source</option> + <option value="id" selected="true">id</option> + <option value="name" selected="true">name</option> + <validator type="no_options" message="Please select at least one field" /> + </param> + <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> + <param name="query_field" type="select" label="Fields" > + <option value="BIOSAMPLE">BIOSAMPLE</option> + <option value="PROJECT">PROJECT</option> + <option value="SAMPLE">SAMPLE</option> + <option value="TAXON">TAXON</option> + <option value="common_name">common_name</option> + <option value="description">description</option> + <option value="domain_source">domain_source</option> + <option value="id">id</option> + <option value="id_noversion">id_noversion</option> + <option value="name">name</option> + <option value="project_description">project_description</option> + <option value="scientific_name">scientific_name</option> + <option value="set_chain">set_chain</option> + <option value="strain">strain</option> + </param> + <conditional name="comp_operation"> + <param name="operation" type="select" label="Comparison operation" > + <option value="equal">equal</option> + <option value="not">not</option> + <option value="range">range</option> + </param> + <when value="equal"> + <param name="query_text" type="text" label="Searched term"/> + </when> + <when value="not"> + <param name="query_text" type="text" label="Searched term"/> + <param name="not_query_text" type="text" label="Limiting term"/> + </when> + <when value="range"> + <param name="min" type="text" label="From"/> + <param name="max" type="text" label="To"/> + </when> + </conditional> + </repeat> + </when> + + <when value="wgs_masters"> + <param name="fields" type="select" label="Fields to extract" multiple="true"> + <option value="BIOSAMPLE" selected="true">BIOSAMPLE</option> + <option value="PROJECT" selected="true">PROJECT</option> + <option value="PUBMED" selected="true">PUBMED</option> + <option value="SAMPLE" selected="true">SAMPLE</option> + <option value="TAXON" selected="true">TAXON</option> + <option value="acc" selected="true">acc</option> + <option value="description" selected="true">description</option> + <option value="domain_source" selected="true">domain_source</option> + <option value="id" selected="true">id</option> + <validator type="no_options" message="Please select at least one field" /> + </param> + <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> + <param name="query_field" type="select" label="Fields" > + <option value="BIOSAMPLE">BIOSAMPLE</option> + <option value="PROJECT">PROJECT</option> + <option value="PUBMED">PUBMED</option> + <option value="SAMPLE">SAMPLE</option> + <option value="TAXON">TAXON</option> + <option value="acc">acc</option> + <option value="bio_material">bio_material</option> + <option value="common_name">common_name</option> + <option value="creation_date">creation_date</option> + <option value="culture_collection">culture_collection</option> + <option value="description">description</option> + <option value="division">division</option> + <option value="domain_source">domain_source</option> + <option value="host">host</option> + <option value="id">id</option> + <option value="isolate">isolate</option> + <option value="isolation_source">isolation_source</option> + <option value="keywords">keywords</option> + <option value="last_modification_date">last_modification_date</option> + <option value="molecule_type">molecule_type</option> + <option value="prefix">prefix</option> + <option value="scientific_name">scientific_name</option> + <option value="specimen_voucher">specimen_voucher</option> + <option value="strain">strain</option> + </param> + <conditional name="comp_operation"> + <param name="operation" type="select" label="Comparison operation" > + <option value="equal">equal</option> + <option value="not">not</option> + <option value="range">range</option> + </param> + <when value="equal"> + <param name="query_text" type="text" label="Searched term"/> + </when> + <when value="not"> + <param name="query_text" type="text" label="Searched term"/> + <param name="not_query_text" type="text" label="Limiting term"/> + </when> + <when value="range"> + <param name="min" type="text" label="From"/> + <param name="max" type="text" label="To"/> + </when> + </conditional> + </repeat> + </when> + + <when value="emblrelease_con"> + <param name="fields" type="select" label="Fields to extract" multiple="true"> + <option value="BIOSAMPLE" selected="true">BIOSAMPLE</option> + <option value="CABRI" selected="true">CABRI</option> + <option value="DOI" selected="true">DOI</option> + <option value="EC" selected="true">EC</option> + <option value="EMBLCDS" selected="true">EMBLCDS</option> + <option value="ENA" selected="true">ENA</option> + <option value="ENA-CON" selected="true">ENA-CON</option> + <option value="ENSEMBL-GN" selected="true">ENSEMBL-GN</option> + <option value="ENSEMBLGENOMES-GN" selected="true">ENSEMBLGENOMES-GN</option> + <option value="EUROPEPMC" selected="true">EUROPEPMC</option> + <option value="FLYBASE" selected="true">FLYBASE</option> + <option value="GOA" selected="true">GOA</option> + <option value="GRAINGENES" selected="true">GRAINGENES</option> + <option value="HGNC" selected="true">HGNC</option> + <option value="INTERPRO" selected="true">INTERPRO</option> + <option value="MGI" selected="true">MGI</option> + <option value="PDB" selected="true">PDB</option> + <option value="PUBMED" selected="true">PUBMED</option> + <option value="STRAININFO" selected="true">STRAININFO</option> + <option value="TAXON" selected="true">TAXON</option> + <option value="UNIPROTKB_SWISS-PROT" selected="true">UNIPROTKB_SWISS-PROT</option> + <option value="UNIPROTKB_TREMBL" selected="true">UNIPROTKB_TREMBL</option> + <option value="VECTORBASE" selected="true">VECTORBASE</option> + <option value="WORMBASE" selected="true">WORMBASE</option> + <option value="ZFIN" selected="true">ZFIN</option> + <option value="acc" selected="true">acc</option> + <option value="description" selected="true">description</option> + <option value="domain_source" selected="true">domain_source</option> + <option value="id" selected="true">id</option> + <validator type="no_options" message="Please select at least one field" /> + </param> + <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> + <param name="query_field" type="select" label="Fields" > + <option value="BIOSAMPLE">BIOSAMPLE</option> + <option value="CABRI">CABRI</option> + <option value="DOI">DOI</option> + <option value="EC">EC</option> + <option value="EMBLCDS">EMBLCDS</option> + <option value="EMBLCDS_version">EMBLCDS_version</option> + <option value="ENA">ENA</option> + <option value="ENA-CON">ENA-CON</option> + <option value="ENSEMBL-GN">ENSEMBL-GN</option> + <option value="ENSEMBL-SCAFFOLDS">ENSEMBL-SCAFFOLDS</option> + <option value="ENSEMBL-TR">ENSEMBL-TR</option> + <option value="ENSEMBLGENOMES-GN">ENSEMBLGENOMES-GN</option> + <option value="ENSEMBLGENOMES-TR">ENSEMBLGENOMES-TR</option> + <option value="EUROPEPMC">EUROPEPMC</option> + <option value="FLYBASE">FLYBASE</option> + <option value="GOA">GOA</option> + <option value="GRAINGENES">GRAINGENES</option> + <option value="HGNC">HGNC</option> + <option value="INTERPRO">INTERPRO</option> + <option value="MD5">MD5</option> + <option value="MGI">MGI</option> + <option value="PDB">PDB</option> + <option value="PROJECT">PROJECT</option> + <option value="PSEUDO">PSEUDO</option> + <option value="PUBMED">PUBMED</option> + <option value="STRAININFO">STRAININFO</option> + <option value="TAXON">TAXON</option> + <option value="UNIPROTKB_SWISS-PROT">UNIPROTKB_SWISS-PROT</option> + <option value="UNIPROTKB_TREMBL">UNIPROTKB_TREMBL</option> + <option value="VECTORBASE">VECTORBASE</option> + <option value="WORMBASE">WORMBASE</option> + <option value="ZFIN">ZFIN</option> + <option value="acc">acc</option> + <option value="bio_material">bio_material</option> + <option value="creation_date">creation_date</option> + <option value="culture_collection">culture_collection</option> + <option value="data_class">data_class</option> + <option value="description">description</option> + <option value="division">division</option> + <option value="domain_source">domain_source</option> + <option value="gene">gene</option> + <option value="gene_synonym">gene_synonym</option> + <option value="id">id</option> + <option value="keywords">keywords</option> + <option value="last_modification_date">last_modification_date</option> + <option value="length">length</option> + <option value="locus_tag">locus_tag</option> + <option value="molecule_type">molecule_type</option> + <option value="old_locus_tag">old_locus_tag</option> + <option value="organelle">organelle</option> + <option value="organism">organism</option> + <option value="organism_classification">organism_classification</option> + <option value="organism_species">organism_species</option> + <option value="product">product</option> + <option value="references">references</option> + <option value="sequence_version">sequence_version</option> + <option value="specimen_voucher">specimen_voucher</option> + <option value="topology">topology</option> + </param> + <conditional name="comp_operation"> + <param name="operation" type="select" label="Comparison operation" > + <option value="equal">equal</option> + <option value="not">not</option> + <option value="range">range</option> + </param> + <when value="equal"> + <param name="query_text" type="text" label="Searched term"/> + </when> + <when value="not"> + <param name="query_text" type="text" label="Searched term"/> + <param name="not_query_text" type="text" label="Limiting term"/> + </when> + <when value="range"> + <param name="min" type="text" label="From"/> + <param name="max" type="text" label="To"/> + </when> + </conditional> + </repeat> + </when> + + <when value="emblnew_con"> + <param name="fields" type="select" label="Fields to extract" multiple="true"> + <option value="BIOSAMPLE" selected="true">BIOSAMPLE</option> + <option value="DOI" selected="true">DOI</option> + <option value="EC" selected="true">EC</option> + <option value="EMBLCDS" selected="true">EMBLCDS</option> + <option value="ENA" selected="true">ENA</option> + <option value="ENA-CON" selected="true">ENA-CON</option> + <option value="ENSEMBL-GN" selected="true">ENSEMBL-GN</option> + <option value="ENSEMBLGENOMES-GN" selected="true">ENSEMBLGENOMES-GN</option> + <option value="EUROPEPMC" selected="true">EUROPEPMC</option> + <option value="GOA" selected="true">GOA</option> + <option value="INTERPRO" selected="true">INTERPRO</option> + <option value="PDB" selected="true">PDB</option> + <option value="PUBMED" selected="true">PUBMED</option> + <option value="TAXON" selected="true">TAXON</option> + <option value="UNIPROTKB_SWISS-PROT" selected="true">UNIPROTKB_SWISS-PROT</option> + <option value="UNIPROTKB_TREMBL" selected="true">UNIPROTKB_TREMBL</option> + <option value="WORMBASE" selected="true">WORMBASE</option> + <option value="acc" selected="true">acc</option> + <option value="description" selected="true">description</option> + <option value="domain_source" selected="true">domain_source</option> + <option value="id" selected="true">id</option> + <validator type="no_options" message="Please select at least one field" /> + </param> + <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> + <param name="query_field" type="select" label="Fields" > + <option value="BIOSAMPLE">BIOSAMPLE</option> + <option value="DOI">DOI</option> + <option value="EC">EC</option> + <option value="EMBLCDS">EMBLCDS</option> + <option value="EMBLCDS_version">EMBLCDS_version</option> + <option value="ENA">ENA</option> + <option value="ENA-CON">ENA-CON</option> + <option value="ENSEMBL-GN">ENSEMBL-GN</option> + <option value="ENSEMBL-SCAFFOLDS">ENSEMBL-SCAFFOLDS</option> + <option value="ENSEMBL-TR">ENSEMBL-TR</option> + <option value="ENSEMBLGENOMES-GN">ENSEMBLGENOMES-GN</option> + <option value="ENSEMBLGENOMES-TR">ENSEMBLGENOMES-TR</option> + <option value="EUROPEPMC">EUROPEPMC</option> + <option value="GOA">GOA</option> + <option value="INTERPRO">INTERPRO</option> + <option value="MD5">MD5</option> + <option value="PDB">PDB</option> + <option value="PROJECT">PROJECT</option> + <option value="PSEUDO">PSEUDO</option> + <option value="PUBMED">PUBMED</option> + <option value="TAXON">TAXON</option> + <option value="UNIPROTKB_SWISS-PROT">UNIPROTKB_SWISS-PROT</option> + <option value="UNIPROTKB_TREMBL">UNIPROTKB_TREMBL</option> + <option value="WORMBASE">WORMBASE</option> + <option value="acc">acc</option> + <option value="bio_material">bio_material</option> + <option value="creation_date">creation_date</option> + <option value="culture_collection">culture_collection</option> + <option value="data_class">data_class</option> + <option value="description">description</option> + <option value="division">division</option> + <option value="domain_source">domain_source</option> + <option value="gene">gene</option> + <option value="id">id</option> + <option value="keywords">keywords</option> + <option value="last_modification_date">last_modification_date</option> + <option value="length">length</option> + <option value="locus_tag">locus_tag</option> + <option value="molecule_type">molecule_type</option> + <option value="organelle">organelle</option> + <option value="organism">organism</option> + <option value="organism_classification">organism_classification</option> + <option value="organism_species">organism_species</option> + <option value="product">product</option> + <option value="references">references</option> + <option value="sequence_version">sequence_version</option> + <option value="topology">topology</option> + </param> + <conditional name="comp_operation"> + <param name="operation" type="select" label="Comparison operation" > + <option value="equal">equal</option> + <option value="not">not</option> + <option value="range">range</option> + </param> + <when value="equal"> + <param name="query_text" type="text" label="Searched term"/> + </when> + <when value="not"> + <param name="query_text" type="text" label="Searched term"/> + <param name="not_query_text" type="text" label="Limiting term"/> + </when> + <when value="range"> + <param name="min" type="text" label="From"/> + <param name="max" type="text" label="To"/> + </when> + </conditional> + </repeat> + </when> + + <when value="atlas-genes"> + <param name="fields" type="select" label="Fields to extract" multiple="true"> + <option value="ATLAS" selected="true">ATLAS</option> + <option value="EMBL" selected="true">EMBL</option> + <option value="ENSFAMILY" selected="true">ENSFAMILY</option> + <option value="ENSPROTEIN" selected="true">ENSPROTEIN</option> + <option value="ENTREZGENE" selected="true">ENTREZGENE</option> + <option value="GO" selected="true">GO</option> + <option value="INTERPRO" selected="true">INTERPRO</option> + <option value="REFSEQ" selected="true">REFSEQ</option> + <option value="TAXONOMY" selected="true">TAXONOMY</option> + <option value="UNIGENE" selected="true">UNIGENE</option> + <option value="UNIPROT" selected="true">UNIPROT</option> + <option value="description" selected="true">description</option> + <option value="domain_source" selected="true">domain_source</option> + <option value="id" selected="true">id</option> + <option value="name" selected="true">name</option> + <option value="organism_part" selected="true">organism_part</option> + <validator type="no_options" message="Please select at least one field" /> + </param> + <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> + <param name="query_field" type="select" label="Fields" > + <option value="ATLAS">ATLAS</option> + <option value="EMBL">EMBL</option> + <option value="ENSFAMILY">ENSFAMILY</option> + <option value="ENSPROTEIN">ENSPROTEIN</option> + <option value="ENSTRANSCRIPT">ENSTRANSCRIPT</option> + <option value="ENTREZGENE">ENTREZGENE</option> + <option value="GO">GO</option> + <option value="INTERPRO">INTERPRO</option> + <option value="REFSEQ">REFSEQ</option> + <option value="TAXONOMY">TAXONOMY</option> + <option value="UNIGENE">UNIGENE</option> + <option value="UNIPROT">UNIPROT</option> + <option value="age">age</option> + <option value="breed">breed</option> + <option value="cell_line">cell_line</option> + <option value="cell_type">cell_type</option> + <option value="cellular_component">cellular_component</option> + <option value="cultivar">cultivar</option> + <option value="description">description</option> + <option value="developmental_stage">developmental_stage</option> + <option value="disease">disease</option> + <option value="domain_source">domain_source</option> + <option value="ecotype">ecotype</option> + <option value="ensfamily_description">ensfamily_description</option> + <option value="gene_biotype">gene_biotype</option> + <option value="goterm">goterm</option> + <option value="hgnc_symbol">hgnc_symbol</option> + <option value="id">id</option> + <option value="id_noversion">id_noversion</option> + <option value="individual">individual</option> + <option value="interproterm">interproterm</option> + <option value="mirbase_accession">mirbase_accession</option> + <option value="mirbase_id">mirbase_id</option> + <option value="name">name</option> + <option value="organism_part">organism_part</option> + <option value="ortholog">ortholog</option> + <option value="phenotype">phenotype</option> + <option value="rna">rna</option> + <option value="sampling_time_point">sampling_time_point</option> + <option value="sex">sex</option> + <option value="somite_stage">somite_stage</option> + <option value="strain">strain</option> + <option value="synonym">synonym</option> + </param> + <conditional name="comp_operation"> + <param name="operation" type="select" label="Comparison operation" > + <option value="equal">equal</option> + <option value="not">not</option> + <option value="range">range</option> + </param> + <when value="equal"> + <param name="query_text" type="text" label="Searched term"/> + </when> + <when value="not"> + <param name="query_text" type="text" label="Searched term"/> + <param name="not_query_text" type="text" label="Limiting term"/> + </when> + <when value="range"> + <param name="min" type="text" label="From"/> + <param name="max" type="text" label="To"/> + </when> + </conditional> + </repeat> + </when> + + <when value="biomodels"> + <param name="fields" type="select" label="Fields to extract" multiple="true"> + <option value="3DMET" selected="true">3DMET</option> + <option value="BIND" selected="true">BIND</option> + <option value="BIOMODELSDATABASE" selected="true">BIOMODELSDATABASE</option> + <option value="BRENDA" selected="true">BRENDA</option> + <option value="BRENDATISSUEONTOLOGY" selected="true">BRENDATISSUEONTOLOGY</option> + <option value="CAS" selected="true">CAS</option> + <option value="CELLCYCLEONTOLOGY" selected="true">CELLCYCLEONTOLOGY</option> + <option value="CELLTYPEONTOLOGY" selected="true">CELLTYPEONTOLOGY</option> + <option value="CHEBI" selected="true">CHEBI</option> + <option value="CHEMBLCOMPOUND" selected="true">CHEMBLCOMPOUND</option> + <option value="DOI" selected="true">DOI</option> + <option value="ENSEMBL" selected="true">ENSEMBL</option> + <option value="ENZYMENOMENCLATURE" selected="true">ENZYMENOMENCLATURE</option> + <option value="EVIDENCECODEONTOLOGY" selected="true">EVIDENCECODEONTOLOGY</option> + <option value="EXPERIMENTALFACTORONTOLOGY" selected="true">EXPERIMENTALFACTORONTOLOGY</option> + <option value="FMA" selected="true">FMA</option> + <option value="GENEONTOLOGY" selected="true">GENEONTOLOGY</option> + <option value="HGNCSYMBOL" selected="true">HGNCSYMBOL</option> + <option value="HUMANDISEASEONTOLOGY" selected="true">HUMANDISEASEONTOLOGY</option> + <option value="ICD" selected="true">ICD</option> + <option value="INTACT" selected="true">INTACT</option> + <option value="INTERPRO" selected="true">INTERPRO</option> + <option value="ISBN" selected="true">ISBN</option> + <option value="KEGGCOMPOUND" selected="true">KEGGCOMPOUND</option> + <option value="KEGGDRUG" selected="true">KEGGDRUG</option> + <option value="KEGGGENES" selected="true">KEGGGENES</option> + <option value="KEGGGENOME" selected="true">KEGGGENOME</option> + <option value="KEGGORTHOLOGY" selected="true">KEGGORTHOLOGY</option> + <option value="KEGGPATHWAY" selected="true">KEGGPATHWAY</option> + <option value="KEGGREACTION" selected="true">KEGGREACTION</option> + <option value="LIPIDMAPS" selected="true">LIPIDMAPS</option> + <option value="MATHEMATICALMODELLINGONTOLOGY" selected="true">MATHEMATICALMODELLINGONTOLOGY</option> + <option value="MIRBASESEQUENCE" selected="true">MIRBASESEQUENCE</option> + <option value="MOLECULARINTERACTIONSONTOLOGY" selected="true">MOLECULARINTERACTIONSONTOLOGY</option> + <option value="NARCIS" selected="true">NARCIS</option> + <option value="NCBIGENE" selected="true">NCBIGENE</option> + <option value="NCBIPROTEIN" selected="true">NCBIPROTEIN</option> + <option value="NUCLEOTIDESEQUENCEDATABASE" selected="true">NUCLEOTIDESEQUENCEDATABASE</option> + <option value="OMIM" selected="true">OMIM</option> + <option value="ONTOLOGYOFPHYSICSFORBIOLOGY" selected="true">ONTOLOGYOFPHYSICSFORBIOLOGY</option> + <option value="PANTHERPATHWAY" selected="true">PANTHERPATHWAY</option> + <option value="PATHWAYONTOLOGY" selected="true">PATHWAYONTOLOGY</option> + <option value="PATO" selected="true">PATO</option> + <option value="PIRSF" selected="true">PIRSF</option> + <option value="PROTEINMODIFICATIONONTOLOGY" selected="true">PROTEINMODIFICATIONONTOLOGY</option> + <option value="PROTEINONTOLOGY" selected="true">PROTEINONTOLOGY</option> + <option value="PUBCHEM-COMPOUND" selected="true">PUBCHEM-COMPOUND</option> + <option value="PUBCHEM-SUBSTANCE" selected="true">PUBCHEM-SUBSTANCE</option> + <option value="PUBMED" selected="true">PUBMED</option> + <option value="REACTOME" selected="true">REACTOME</option> + <option value="SEQUENCEONTOLOGY" selected="true">SEQUENCEONTOLOGY</option> + <option value="SGD" selected="true">SGD</option> + <option value="SUBTIWIKI" selected="true">SUBTIWIKI</option> + <option value="SYSTEMSBIOLOGYONTOLOGY" selected="true">SYSTEMSBIOLOGYONTOLOGY</option> + <option value="TAXONOMY" selected="true">TAXONOMY</option> + <option value="TRANSPORTCLASSIFICATIONDATABASE" selected="true">TRANSPORTCLASSIFICATIONDATABASE</option> + <option value="UNIPROT" selected="true">UNIPROT</option> + <option value="UNIPROTISOFORM" selected="true">UNIPROTISOFORM</option> + <option value="URL" selected="true">URL</option> + <option value="description" selected="true">description</option> + <option value="domain_source" selected="true">domain_source</option> + <option value="id" selected="true">id</option> + <option value="name" selected="true">name</option> + <validator type="no_options" message="Please select at least one field" /> + </param> + <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> + <param name="query_field" type="select" label="Fields" > + <option value="3DMET">3DMET</option> + <option value="BIND">BIND</option> + <option value="BIOMODELSDATABASE">BIOMODELSDATABASE</option> + <option value="BRENDA">BRENDA</option> + <option value="BRENDATISSUEONTOLOGY">BRENDATISSUEONTOLOGY</option> + <option value="CAS">CAS</option> + <option value="CELLCYCLEONTOLOGY">CELLCYCLEONTOLOGY</option> + <option value="CELLTYPEONTOLOGY">CELLTYPEONTOLOGY</option> + <option value="CHEBI">CHEBI</option> + <option value="CHEMBLCOMPOUND">CHEMBLCOMPOUND</option> + <option value="DOI">DOI</option> + <option value="ENSEMBL">ENSEMBL</option> + <option value="ENZYMENOMENCLATURE">ENZYMENOMENCLATURE</option> + <option value="EVIDENCECODEONTOLOGY">EVIDENCECODEONTOLOGY</option> + <option value="EXPERIMENTALFACTORONTOLOGY">EXPERIMENTALFACTORONTOLOGY</option> + <option value="FMA">FMA</option> + <option value="GENEONTOLOGY">GENEONTOLOGY</option> + <option value="HGNCSYMBOL">HGNCSYMBOL</option> + <option value="HUMANDISEASEONTOLOGY">HUMANDISEASEONTOLOGY</option> + <option value="ICD">ICD</option> + <option value="INTACT">INTACT</option> + <option value="INTERPRO">INTERPRO</option> + <option value="ISBN">ISBN</option> + <option value="KEGGCOMPOUND">KEGGCOMPOUND</option> + <option value="KEGGDRUG">KEGGDRUG</option> + <option value="KEGGGENES">KEGGGENES</option> + <option value="KEGGGENOME">KEGGGENOME</option> + <option value="KEGGORTHOLOGY">KEGGORTHOLOGY</option> + <option value="KEGGPATHWAY">KEGGPATHWAY</option> + <option value="KEGGREACTION">KEGGREACTION</option> + <option value="LIPIDMAPS">LIPIDMAPS</option> + <option value="MATHEMATICALMODELLINGONTOLOGY">MATHEMATICALMODELLINGONTOLOGY</option> + <option value="MIRBASESEQUENCE">MIRBASESEQUENCE</option> + <option value="MOLECULARINTERACTIONSONTOLOGY">MOLECULARINTERACTIONSONTOLOGY</option> + <option value="NARCIS">NARCIS</option> + <option value="NCBIGENE">NCBIGENE</option> + <option value="NCBIPROTEIN">NCBIPROTEIN</option> + <option value="NUCLEOTIDESEQUENCEDATABASE">NUCLEOTIDESEQUENCEDATABASE</option> + <option value="OMIM">OMIM</option> + <option value="ONTOLOGYOFPHYSICSFORBIOLOGY">ONTOLOGYOFPHYSICSFORBIOLOGY</option> + <option value="PANTHERPATHWAY">PANTHERPATHWAY</option> + <option value="PATHWAYONTOLOGY">PATHWAYONTOLOGY</option> + <option value="PATO">PATO</option> + <option value="PIRSF">PIRSF</option> + <option value="PROTEINMODIFICATIONONTOLOGY">PROTEINMODIFICATIONONTOLOGY</option> + <option value="PROTEINONTOLOGY">PROTEINONTOLOGY</option> + <option value="PUBCHEM-COMPOUND">PUBCHEM-COMPOUND</option> + <option value="PUBCHEM-SUBSTANCE">PUBCHEM-SUBSTANCE</option> + <option value="PUBMED">PUBMED</option> + <option value="REACTOME">REACTOME</option> + <option value="SEQUENCEONTOLOGY">SEQUENCEONTOLOGY</option> + <option value="SGD">SGD</option> + <option value="SUBTIWIKI">SUBTIWIKI</option> + <option value="SYSTEMSBIOLOGYONTOLOGY">SYSTEMSBIOLOGYONTOLOGY</option> + <option value="TAXONOMY">TAXONOMY</option> + <option value="TRANSPORTCLASSIFICATIONDATABASE">TRANSPORTCLASSIFICATIONDATABASE</option> + <option value="UNIPROT">UNIPROT</option> + <option value="UNIPROTISOFORM">UNIPROTISOFORM</option> + <option value="URL">URL</option> + <option value="acc">acc</option> + <option value="author">author</option> + <option value="brenda_name">brenda_name</option> + <option value="cco_name">cco_name</option> + <option value="chebi_name">chebi_name</option> + <option value="cl_name">cl_name</option> + <option value="creation_date">creation_date</option> + <option value="curated">curated</option> + <option value="description">description</option> + <option value="doid_name">doid_name</option> + <option value="domain_source">domain_source</option> + <option value="eco_name">eco_name</option> + <option value="efo_name">efo_name</option> + <option value="fma_name">fma_name</option> + <option value="go_name">go_name</option> + <option value="id">id</option> + <option value="kegg_compound_name">kegg_compound_name</option> + <option value="kegg_genes_name">kegg_genes_name</option> + <option value="kegg_genome_definition">kegg_genome_definition</option> + <option value="kegg_orthology_name">kegg_orthology_name</option> + <option value="kegg_pathway_name">kegg_pathway_name</option> + <option value="kegg_reaction_name">kegg_reaction_name</option> + <option value="keywords">keywords</option> + <option value="last_modification_date">last_modification_date</option> + <option value="mi_name">mi_name</option> + <option value="mod_name">mod_name</option> + <option value="name">name</option> + <option value="omim_name">omim_name</option> + <option value="original_model">original_model</option> + <option value="other_name">other_name</option> + <option value="pato_name">pato_name</option> + <option value="pro_name">pro_name</option> + <option value="publication_title">publication_title</option> + <option value="pw_name">pw_name</option> + <option value="sbo_name">sbo_name</option> + <option value="so_name">so_name</option> + <option value="species">species</option> + <option value="uniprot_name">uniprot_name</option> + </param> + <conditional name="comp_operation"> + <param name="operation" type="select" label="Comparison operation" > + <option value="equal">equal</option> + <option value="not">not</option> + <option value="range">range</option> + </param> + <when value="equal"> + <param name="query_text" type="text" label="Searched term"/> + </when> + <when value="not"> + <param name="query_text" type="text" label="Searched term"/> + <param name="not_query_text" type="text" label="Limiting term"/> + </when> + <when value="range"> + <param name="min" type="text" label="From"/> + <param name="max" type="text" label="To"/> + </when> + </conditional> + </repeat> + </when> + + <when value="biosamples"> + <param name="fields" type="select" label="Fields to extract" multiple="true"> + <option value="description" selected="true">description</option> + <option value="domain_source" selected="true">domain_source</option> + <option value="id" selected="true">id</option> + <option value="name" selected="true">name</option> + <validator type="no_options" message="Please select at least one field" /> + </param> + <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> + <param name="query_field" type="select" label="Fields" > + <option value="acc">acc</option> + <option value="description">description</option> + <option value="domain_source">domain_source</option> + <option value="id">id</option> + <option value="name">name</option> + <option value="searchwords">searchwords</option> + </param> + <conditional name="comp_operation"> + <param name="operation" type="select" label="Comparison operation" > + <option value="equal">equal</option> + <option value="not">not</option> + <option value="range">range</option> + </param> + <when value="equal"> + <param name="query_text" type="text" label="Searched term"/> + </when> + <when value="not"> + <param name="query_text" type="text" label="Searched term"/> + <param name="not_query_text" type="text" label="Limiting term"/> + </when> + <when value="range"> + <param name="min" type="text" label="From"/> + <param name="max" type="text" label="To"/> + </when> + </conditional> + </repeat> + </when> + + <when value="biosamples-groups"> + <param name="fields" type="select" label="Fields to extract" multiple="true"> + <option value="description" selected="true">description</option> + <option value="domain_source" selected="true">domain_source</option> + <option value="id" selected="true">id</option> + <option value="name" selected="true">name</option> + <validator type="no_options" message="Please select at least one field" /> + </param> + <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> + <param name="query_field" type="select" label="Fields" > + <option value="acc">acc</option> + <option value="description">description</option> + <option value="domain_source">domain_source</option> + <option value="id">id</option> + <option value="name">name</option> + <option value="searchwords">searchwords</option> + </param> + <conditional name="comp_operation"> + <param name="operation" type="select" label="Comparison operation" > + <option value="equal">equal</option> + <option value="not">not</option> + <option value="range">range</option> + </param> + <when value="equal"> + <param name="query_text" type="text" label="Searched term"/> + </when> + <when value="not"> + <param name="query_text" type="text" label="Searched term"/> + <param name="not_query_text" type="text" label="Limiting term"/> + </when> + <when value="range"> + <param name="min" type="text" label="From"/> + <param name="max" type="text" label="To"/> + </when> + </conditional> + </repeat> + </when> + + <when value="chebi"> + <param name="fields" type="select" label="Fields to extract" multiple="true"> + <option value="ARRAYEXPRESS" selected="true">ARRAYEXPRESS</option> + <option value="ARRAYEXPRESSATLAS" selected="true">ARRAYEXPRESSATLAS</option> + <option value="BIOMODELS" selected="true">BIOMODELS</option> + <option value="BRENDA" selected="true">BRENDA</option> + <option value="CAS_REGISTRY_NUMBER" selected="true">CAS_REGISTRY_NUMBER</option> + <option value="CHEMBL" selected="true">CHEMBL</option> + <option value="CHEMIDPLUS" selected="true">CHEMIDPLUS</option> + <option value="CHEMSPIDER" selected="true">CHEMSPIDER</option> + <option value="CHINESE_ABSTRACTS_CITATION" selected="true">CHINESE_ABSTRACTS_CITATION</option> + <option value="CITEXPLORE_CITATION" selected="true">CITEXPLORE_CITATION</option> + <option value="COME" selected="true">COME</option> + <option value="COMPTOX" selected="true">COMPTOX</option> + <option value="DRUGBANK" selected="true">DRUGBANK</option> + <option value="ECMDB" selected="true">ECMDB</option> + <option value="ENZYMEPORTAL" selected="true">ENZYMEPORTAL</option> + <option value="GOLM" selected="true">GOLM</option> + <option value="HMDB" selected="true">HMDB</option> + <option value="IEDB" selected="true">IEDB</option> + <option value="INTACT" selected="true">INTACT</option> + <option value="INTENZ" selected="true">INTENZ</option> + <option value="KEGG_COMPOUND" selected="true">KEGG_COMPOUND</option> + <option value="KEGG_DRUG" selected="true">KEGG_DRUG</option> + <option value="KEGG_GLYCAN" selected="true">KEGG_GLYCAN</option> + <option value="KNAPSACK" selected="true">KNAPSACK</option> + <option value="LINCS" selected="true">LINCS</option> + <option value="LIPID_MAPS_CLASS" selected="true">LIPID_MAPS_CLASS</option> + <option value="LIPID_MAPS_INSTANCE" selected="true">LIPID_MAPS_INSTANCE</option> + <option value="MASSBANK" selected="true">MASSBANK</option> + <option value="METACYC" selected="true">METACYC</option> + <option value="MOLBASE" selected="true">MOLBASE</option> + <option value="NMRSHIFTDB" selected="true">NMRSHIFTDB</option> + <option value="NURSA" selected="true">NURSA</option> + <option value="PATENT" selected="true">PATENT</option> + <option value="PDB" selected="true">PDB</option> + <option value="PDBECHEM" selected="true">PDBECHEM</option> + <option value="PESTICIDES" selected="true">PESTICIDES</option> + <option value="PUBCHEM" selected="true">PUBCHEM</option> + <option value="PUBMED_CITATION" selected="true">PUBMED_CITATION</option> + <option value="REACTOME" selected="true">REACTOME</option> + <option value="REAXYS_REGISTRY_NUMBER" selected="true">REAXYS_REGISTRY_NUMBER</option> + <option value="RESID" selected="true">RESID</option> + <option value="RHEA" selected="true">RHEA</option> + <option value="SABIO-RK" selected="true">SABIO-RK</option> + <option value="UM-BBD_COMPID" selected="true">UM-BBD_COMPID</option> + <option value="UNIPROT" selected="true">UNIPROT</option> + <option value="WEBELEMENTS" selected="true">WEBELEMENTS</option> + <option value="WIKIPEDIA" selected="true">WIKIPEDIA</option> + <option value="YMDB" selected="true">YMDB</option> + <option value="description" selected="true">description</option> + <option value="domain_source" selected="true">domain_source</option> + <option value="id" selected="true">id</option> + <option value="inchi" selected="true">inchi</option> + <option value="inchikey" selected="true">inchikey</option> + <option value="iupac_name" selected="true">iupac_name</option> + <option value="name" selected="true">name</option> + <option value="smiles" selected="true">smiles</option> + <validator type="no_options" message="Please select at least one field" /> + </param> + <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> + <param name="query_field" type="select" label="Fields" > + <option value="AGRICOLA_CITATION">AGRICOLA_CITATION</option> + <option value="ARRAYEXPRESS">ARRAYEXPRESS</option> + <option value="ARRAYEXPRESSATLAS">ARRAYEXPRESSATLAS</option> + <option value="BEILSTEIN_REGISTRY_NUMBER">BEILSTEIN_REGISTRY_NUMBER</option> + <option value="BIOMODELS">BIOMODELS</option> + <option value="BRENDA">BRENDA</option> + <option value="CAS_REGISTRY_NUMBER">CAS_REGISTRY_NUMBER</option> + <option value="CHEMBL">CHEMBL</option> + <option value="CHEMIDPLUS">CHEMIDPLUS</option> + <option value="CHEMSPIDER">CHEMSPIDER</option> + <option value="CHINESE_ABSTRACTS_CITATION">CHINESE_ABSTRACTS_CITATION</option> + <option value="CITEXPLORE_CITATION">CITEXPLORE_CITATION</option> + <option value="COME">COME</option> + <option value="COMPTOX">COMPTOX</option> + <option value="DRUGBANK">DRUGBANK</option> + <option value="ECMDB">ECMDB</option> + <option value="ENZYMEPORTAL">ENZYMEPORTAL</option> + <option value="ETH">ETH</option> + <option value="GMELIN_REGISTRY_NUMBER">GMELIN_REGISTRY_NUMBER</option> + <option value="GOLM">GOLM</option> + <option value="HMDB">HMDB</option> + <option value="IEDB">IEDB</option> + <option value="INTACT">INTACT</option> + <option value="INTENZ">INTENZ</option> + <option value="KEGG_COMPOUND">KEGG_COMPOUND</option> + <option value="KEGG_DRUG">KEGG_DRUG</option> + <option value="KEGG_GLYCAN">KEGG_GLYCAN</option> + <option value="KNAPSACK">KNAPSACK</option> + <option value="LINCS">LINCS</option> + <option value="LIPID_MAPS_CLASS">LIPID_MAPS_CLASS</option> + <option value="LIPID_MAPS_INSTANCE">LIPID_MAPS_INSTANCE</option> + <option value="MASSBANK">MASSBANK</option> + <option value="METACYC">METACYC</option> + <option value="MOLBASE">MOLBASE</option> + <option value="NMRSHIFTDB">NMRSHIFTDB</option> + <option value="NURSA">NURSA</option> + <option value="PATENT">PATENT</option> + <option value="PDB">PDB</option> + <option value="PDBECHEM">PDBECHEM</option> + <option value="PESTICIDES">PESTICIDES</option> + <option value="PUBCHEM">PUBCHEM</option> + <option value="PUBMED_CENTRAL_CITATION">PUBMED_CENTRAL_CITATION</option> + <option value="PUBMED_CITATION">PUBMED_CITATION</option> + <option value="REACTOME">REACTOME</option> + <option value="REAXYS_REGISTRY_NUMBER">REAXYS_REGISTRY_NUMBER</option> + <option value="RESID">RESID</option> + <option value="RHEA">RHEA</option> + <option value="SABIO-RK">SABIO-RK</option> + <option value="SMID">SMID</option> + <option value="UM-BBD_COMPID">UM-BBD_COMPID</option> + <option value="UNIPROT">UNIPROT</option> + <option value="WEBELEMENTS">WEBELEMENTS</option> + <option value="WIKIPEDIA">WIKIPEDIA</option> + <option value="YMDB">YMDB</option> + <option value="acc">acc</option> + <option value="charge">charge</option> + <option value="description">description</option> + <option value="domain_source">domain_source</option> + <option value="formula">formula</option> + <option value="has_functional_parent">has_functional_parent</option> + <option value="has_parent_hydride">has_parent_hydride</option> + <option value="has_part">has_part</option> + <option value="has_role">has_role</option> + <option value="id">id</option> + <option value="inchi">inchi</option> + <option value="inchikey">inchikey</option> + <option value="is_a">is_a</option> + <option value="is_conjugate_acid_of">is_conjugate_acid_of</option> + <option value="is_conjugate_base_of">is_conjugate_base_of</option> + <option value="is_enantiomer_of">is_enantiomer_of</option> + <option value="is_substituent_group_from">is_substituent_group_from</option> + <option value="is_tautomer_of">is_tautomer_of</option> + <option value="iupac_name">iupac_name</option> + <option value="mass">mass</option> + <option value="name">name</option> + <option value="secondary_accession_number">secondary_accession_number</option> + <option value="smiles">smiles</option> + <option value="synonym">synonym</option> + </param> + <conditional name="comp_operation"> + <param name="operation" type="select" label="Comparison operation" > + <option value="equal">equal</option> + <option value="not">not</option> + <option value="range">range</option> + </param> + <when value="equal"> + <param name="query_text" type="text" label="Searched term"/> + </when> + <when value="not"> + <param name="query_text" type="text" label="Searched term"/> + <param name="not_query_text" type="text" label="Limiting term"/> + </when> + <when value="range"> + <param name="min" type="text" label="From"/> + <param name="max" type="text" label="To"/> + </when> + </conditional> + </repeat> + </when> + + <when value="chembl-activity"> + <param name="fields" type="select" label="Fields to extract" multiple="true"> + <option value="CHEMBL-ASSAY" selected="true">CHEMBL-ASSAY</option> + <option value="CHEMBL-DOCUMENT" selected="true">CHEMBL-DOCUMENT</option> + <option value="CHEMBL-MOLECULE" selected="true">CHEMBL-MOLECULE</option> + <option value="domain_source" selected="true">domain_source</option> + <option value="id" selected="true">id</option> + <option value="standard_type" selected="true">standard_type</option> + <option value="standard_value" selected="true">standard_value</option> + <validator type="no_options" message="Please select at least one field" /> + </param> + <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> + <param name="query_field" type="select" label="Fields" > + <option value="CHEMBL-ASSAY">CHEMBL-ASSAY</option> + <option value="CHEMBL-DOCUMENT">CHEMBL-DOCUMENT</option> + <option value="CHEMBL-MOLECULE">CHEMBL-MOLECULE</option> + <option value="activity_comment">activity_comment</option> + <option value="domain_source">domain_source</option> + <option value="id">id</option> + <option value="pchembl_value">pchembl_value</option> + <option value="published_relation">published_relation</option> + <option value="published_type">published_type</option> + <option value="published_units">published_units</option> + <option value="published_value">published_value</option> + <option value="standard_relation">standard_relation</option> + <option value="standard_type">standard_type</option> + <option value="standard_units">standard_units</option> + <option value="standard_value">standard_value</option> + </param> + <conditional name="comp_operation"> + <param name="operation" type="select" label="Comparison operation" > + <option value="equal">equal</option> + <option value="not">not</option> + <option value="range">range</option> + </param> + <when value="equal"> + <param name="query_text" type="text" label="Searched term"/> + </when> + <when value="not"> + <param name="query_text" type="text" label="Searched term"/> + <param name="not_query_text" type="text" label="Limiting term"/> + </when> + <when value="range"> + <param name="min" type="text" label="From"/> + <param name="max" type="text" label="To"/> + </when> + </conditional> + </repeat> + </when> + + <when value="chembl-assay"> + <param name="fields" type="select" label="Fields to extract" multiple="true"> + <option value="CHEMBL-ACTIVITY" selected="true">CHEMBL-ACTIVITY</option> + <option value="CHEMBL-DOCUMENT" selected="true">CHEMBL-DOCUMENT</option> + <option value="CHEMBL-TARGET" selected="true">CHEMBL-TARGET</option> + <option value="assay_type" selected="true">assay_type</option> + <option value="description" selected="true">description</option> + <option value="domain_source" selected="true">domain_source</option> + <option value="id" selected="true">id</option> + <validator type="no_options" message="Please select at least one field" /> + </param> + <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> + <param name="query_field" type="select" label="Fields" > + <option value="CHEMBL-ACTIVITY">CHEMBL-ACTIVITY</option> + <option value="CHEMBL-DOCUMENT">CHEMBL-DOCUMENT</option> + <option value="CHEMBL-TARGET">CHEMBL-TARGET</option> + <option value="assay_category">assay_category</option> + <option value="assay_source">assay_source</option> + <option value="assay_test_type">assay_test_type</option> + <option value="assay_type">assay_type</option> + <option value="description">description</option> + <option value="domain_source">domain_source</option> + <option value="id">id</option> + <option value="organism">organism</option> + <option value="tax_id">tax_id</option> + </param> + <conditional name="comp_operation"> + <param name="operation" type="select" label="Comparison operation" > + <option value="equal">equal</option> + <option value="not">not</option> + <option value="range">range</option> + </param> + <when value="equal"> + <param name="query_text" type="text" label="Searched term"/> + </when> + <when value="not"> + <param name="query_text" type="text" label="Searched term"/> + <param name="not_query_text" type="text" label="Limiting term"/> + </when> + <when value="range"> + <param name="min" type="text" label="From"/> + <param name="max" type="text" label="To"/> + </when> + </conditional> + </repeat> + </when> + + <when value="chembl-document"> + <param name="fields" type="select" label="Fields to extract" multiple="true"> + <option value="PUBMED" selected="true">PUBMED</option> + <option value="domain_source" selected="true">domain_source</option> + <option value="id" selected="true">id</option> + <option value="title" selected="true">title</option> + <validator type="no_options" message="Please select at least one field" /> + </param> + <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> + <param name="query_field" type="select" label="Fields" > + <option value="PUBMED">PUBMED</option> + <option value="doi">doi</option> + <option value="domain_source">domain_source</option> + <option value="id">id</option> + <option value="issue">issue</option> + <option value="journal">journal</option> + <option value="title">title</option> + <option value="volume">volume</option> + <option value="year">year</option> + </param> + <conditional name="comp_operation"> + <param name="operation" type="select" label="Comparison operation" > + <option value="equal">equal</option> + <option value="not">not</option> + <option value="range">range</option> + </param> + <when value="equal"> + <param name="query_text" type="text" label="Searched term"/> + </when> + <when value="not"> + <param name="query_text" type="text" label="Searched term"/> + <param name="not_query_text" type="text" label="Limiting term"/> + </when> + <when value="range"> + <param name="min" type="text" label="From"/> + <param name="max" type="text" label="To"/> + </when> + </conditional> + </repeat> + </when> + + <when value="chembl-molecule"> + <param name="fields" type="select" label="Fields to extract" multiple="true"> + <option value="CHEMBL-ACTIVITY" selected="true">CHEMBL-ACTIVITY</option> + <option value="alogp" selected="true">alogp</option> + <option value="canonical_smiles" selected="true">canonical_smiles</option> + <option value="domain_source" selected="true">domain_source</option> + <option value="hydrogen_bond_acceptor_count" selected="true">hydrogen_bond_acceptor_count</option> + <option value="hydrogen_bond_donor_count" selected="true">hydrogen_bond_donor_count</option> + <option value="id" selected="true">id</option> + <option value="molecular_weight" selected="true">molecular_weight</option> + <option value="polar_surface_area" selected="true">polar_surface_area</option> + <validator type="no_options" message="Please select at least one field" /> + </param> + <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> + <param name="query_field" type="select" label="Fields" > + <option value="CHEMBL-ACTIVITY">CHEMBL-ACTIVITY</option> + <option value="alogp">alogp</option> + <option value="canonical_smiles">canonical_smiles</option> + <option value="domain_source">domain_source</option> + <option value="hydrogen_bond_acceptor_count">hydrogen_bond_acceptor_count</option> + <option value="hydrogen_bond_donor_count">hydrogen_bond_donor_count</option> + <option value="id">id</option> + <option value="molecular_species">molecular_species</option> + <option value="molecular_weight">molecular_weight</option> + <option value="molecule_synonym">molecule_synonym</option> + <option value="molecule_type">molecule_type</option> + <option value="molformula">molformula</option> + <option value="polar_surface_area">polar_surface_area</option> + <option value="pref_name">pref_name</option> + <option value="standard_inchi_key">standard_inchi_key</option> + <option value="structure_type">structure_type</option> + </param> + <conditional name="comp_operation"> + <param name="operation" type="select" label="Comparison operation" > + <option value="equal">equal</option> + <option value="not">not</option> + <option value="range">range</option> + </param> + <when value="equal"> + <param name="query_text" type="text" label="Searched term"/> + </when> + <when value="not"> + <param name="query_text" type="text" label="Searched term"/> + <param name="not_query_text" type="text" label="Limiting term"/> + </when> + <when value="range"> + <param name="min" type="text" label="From"/> + <param name="max" type="text" label="To"/> + </when> + </conditional> + </repeat> + </when> + + <when value="chembl-target"> + <param name="fields" type="select" label="Fields to extract" multiple="true"> + <option value="CHEMBL-ASSAY" selected="true">CHEMBL-ASSAY</option> + <option value="CHEMBL-TARGETCOMPONENTS" selected="true">CHEMBL-TARGETCOMPONENTS</option> + <option value="domain_source" selected="true">domain_source</option> + <option value="id" selected="true">id</option> + <option value="organism" selected="true">organism</option> + <validator type="no_options" message="Please select at least one field" /> + </param> + <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> + <param name="query_field" type="select" label="Fields" > + <option value="CHEMBL-ASSAY">CHEMBL-ASSAY</option> + <option value="CHEMBL-TARGETCOMPONENTS">CHEMBL-TARGETCOMPONENTS</option> + <option value="domain_source">domain_source</option> + <option value="id">id</option> + <option value="organism">organism</option> + <option value="parent_target_type">parent_target_type</option> + <option value="pref_name">pref_name</option> + <option value="target_type">target_type</option> + <option value="tax_id">tax_id</option> + </param> + <conditional name="comp_operation"> + <param name="operation" type="select" label="Comparison operation" > + <option value="equal">equal</option> + <option value="not">not</option> + <option value="range">range</option> + </param> + <when value="equal"> + <param name="query_text" type="text" label="Searched term"/> + </when> + <when value="not"> + <param name="query_text" type="text" label="Searched term"/> + <param name="not_query_text" type="text" label="Limiting term"/> + </when> + <when value="range"> + <param name="min" type="text" label="From"/> + <param name="max" type="text" label="To"/> + </when> + </conditional> + </repeat> + </when> + + <when value="chembl-target_component"> + <param name="fields" type="select" label="Fields to extract" multiple="true"> + <option value="CHEMBL-TARGET" selected="true">CHEMBL-TARGET</option> + <option value="accession" selected="true">accession</option> + <option value="component_synonym" selected="true">component_synonym</option> + <option value="component_type" selected="true">component_type</option> + <option value="description" selected="true">description</option> + <option value="domain_source" selected="true">domain_source</option> + <option value="id" selected="true">id</option> + <validator type="no_options" message="Please select at least one field" /> + </param> + <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> + <param name="query_field" type="select" label="Fields" > + <option value="CHEMBL-TARGET">CHEMBL-TARGET</option> + <option value="accession">accession</option> + <option value="component_synonym">component_synonym</option> + <option value="component_type">component_type</option> + <option value="description">description</option> + <option value="domain_source">domain_source</option> + <option value="id">id</option> + </param> + <conditional name="comp_operation"> + <param name="operation" type="select" label="Comparison operation" > + <option value="equal">equal</option> + <option value="not">not</option> + <option value="range">range</option> + </param> + <when value="equal"> + <param name="query_text" type="text" label="Searched term"/> + </when> + <when value="not"> + <param name="query_text" type="text" label="Searched term"/> + <param name="not_query_text" type="text" label="Limiting term"/> + </when> + <when value="range"> + <param name="min" type="text" label="From"/> + <param name="max" type="text" label="To"/> + </when> + </conditional> + </repeat> + </when> + + <when value="coding_release"> + <param name="fields" type="select" label="Fields to extract" multiple="true"> + <option value="AGRICOLA" selected="true">AGRICOLA</option> + <option value="BIOSAMPLE" selected="true">BIOSAMPLE</option> + <option value="DICTYBASE" selected="true">DICTYBASE</option> + <option value="DOI" selected="true">DOI</option> + <option value="EC" selected="true">EC</option> + <option value="EMBL" selected="true">EMBL</option> + <option value="EMBLCDS" selected="true">EMBLCDS</option> + <option value="ENSEMBLGENOMES-GN" selected="true">ENSEMBLGENOMES-GN</option> + <option value="GENEDB" selected="true">GENEDB</option> + <option value="GOA" selected="true">GOA</option> + <option value="H-INVDB" selected="true">H-INVDB</option> + <option value="HGNC" selected="true">HGNC</option> + <option value="INTERPRO" selected="true">INTERPRO</option> + <option value="MGI" selected="true">MGI</option> + <option value="PATENT_NUMBER" selected="true">PATENT_NUMBER</option> + <option value="PDB" selected="true">PDB</option> + <option value="POMBASE" selected="true">POMBASE</option> + <option value="PROJECT" selected="true">PROJECT</option> + <option value="PUBMED" selected="true">PUBMED</option> + <option value="SGD" selected="true">SGD</option> + <option value="SUBTILIST" selected="true">SUBTILIST</option> + <option value="TAXON" selected="true">TAXON</option> + <option value="UNILIB" selected="true">UNILIB</option> + <option value="UNIPROTKB_SWISS-PROT" selected="true">UNIPROTKB_SWISS-PROT</option> + <option value="UNIPROTKB_TREMBL" selected="true">UNIPROTKB_TREMBL</option> + <option value="VECTORBASE" selected="true">VECTORBASE</option> + <option value="WORMBASE" selected="true">WORMBASE</option> + <option value="ZFIN" selected="true">ZFIN</option> + <option value="description" selected="true">description</option> + <option value="domain_source" selected="true">domain_source</option> + <option value="id" selected="true">id</option> + <validator type="no_options" message="Please select at least one field" /> + </param> + <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> + <param name="query_field" type="select" label="Fields" > + <option value="AGRICOLA">AGRICOLA</option> + <option value="BIOSAMPLE">BIOSAMPLE</option> + <option value="DICTYBASE">DICTYBASE</option> + <option value="DOI">DOI</option> + <option value="EC">EC</option> + <option value="EMBL">EMBL</option> + <option value="EMBLCDS">EMBLCDS</option> + <option value="EMBLCDS_version">EMBLCDS_version</option> + <option value="ENSEMBLGENOMES-GN">ENSEMBLGENOMES-GN</option> + <option value="ENSEMBLGENOMES-TR">ENSEMBLGENOMES-TR</option> + <option value="GENEDB">GENEDB</option> + <option value="GOA">GOA</option> + <option value="H-INVDB">H-INVDB</option> + <option value="HGNC">HGNC</option> + <option value="IMGT_HLA">IMGT_HLA</option> + <option value="INTERPRO">INTERPRO</option> + <option value="MD5">MD5</option> + <option value="MGI">MGI</option> + <option value="PATENT_NUMBER">PATENT_NUMBER</option> + <option value="PDB">PDB</option> + <option value="POMBASE">POMBASE</option> + <option value="PROJECT">PROJECT</option> + <option value="PUBMED">PUBMED</option> + <option value="SGD">SGD</option> + <option value="SUBTILIST">SUBTILIST</option> + <option value="TAXON">TAXON</option> + <option value="UNILIB">UNILIB</option> + <option value="UNIPROTKB_SWISS-PROT">UNIPROTKB_SWISS-PROT</option> + <option value="UNIPROTKB_TREMBL">UNIPROTKB_TREMBL</option> + <option value="VECTORBASE">VECTORBASE</option> + <option value="WORMBASE">WORMBASE</option> + <option value="ZFIN">ZFIN</option> + <option value="bio_material">bio_material</option> + <option value="creation_date">creation_date</option> + <option value="culture_collection">culture_collection</option> + <option value="data_class">data_class</option> + <option value="description">description</option> + <option value="division">division</option> + <option value="domain_source">domain_source</option> + <option value="gene">gene</option> + <option value="gene_synonym">gene_synonym</option> + <option value="id">id</option> + <option value="keywords">keywords</option> + <option value="last_modification_date">last_modification_date</option> + <option value="length">length</option> + <option value="locus_tag">locus_tag</option> + <option value="molecule_type">molecule_type</option> + <option value="old_locus_tag">old_locus_tag</option> + <option value="organelle">organelle</option> + <option value="organism">organism</option> + <option value="organism_classification">organism_classification</option> + <option value="organism_species">organism_species</option> + <option value="product">product</option> + <option value="references">references</option> + <option value="sequence_version">sequence_version</option> + <option value="specimen_voucher">specimen_voucher</option> + <option value="topology">topology</option> + </param> + <conditional name="comp_operation"> + <param name="operation" type="select" label="Comparison operation" > + <option value="equal">equal</option> + <option value="not">not</option> + <option value="range">range</option> + </param> + <when value="equal"> + <param name="query_text" type="text" label="Searched term"/> + </when> + <when value="not"> + <param name="query_text" type="text" label="Searched term"/> + <param name="not_query_text" type="text" label="Limiting term"/> + </when> + <when value="range"> + <param name="min" type="text" label="From"/> + <param name="max" type="text" label="To"/> + </when> + </conditional> + </repeat> + </when> + + <when value="coding_update"> + <param name="fields" type="select" label="Fields to extract" multiple="true"> + <option value="AGRICOLA" selected="true">AGRICOLA</option> + <option value="BIOSAMPLE" selected="true">BIOSAMPLE</option> + <option value="DOI" selected="true">DOI</option> + <option value="EC" selected="true">EC</option> + <option value="EMBL" selected="true">EMBL</option> + <option value="EMBLCDS" selected="true">EMBLCDS</option> + <option value="ENSEMBLGENOMES-GN" selected="true">ENSEMBLGENOMES-GN</option> + <option value="GOA" selected="true">GOA</option> + <option value="H-INVDB" selected="true">H-INVDB</option> + <option value="HGNC" selected="true">HGNC</option> + <option value="INTERPRO" selected="true">INTERPRO</option> + <option value="MGI" selected="true">MGI</option> + <option value="PATENT_NUMBER" selected="true">PATENT_NUMBER</option> + <option value="PDB" selected="true">PDB</option> + <option value="PROJECT" selected="true">PROJECT</option> + <option value="PUBMED" selected="true">PUBMED</option> + <option value="SGD" selected="true">SGD</option> + <option value="TAXON" selected="true">TAXON</option> + <option value="UNIPROTKB_SWISS-PROT" selected="true">UNIPROTKB_SWISS-PROT</option> + <option value="UNIPROTKB_TREMBL" selected="true">UNIPROTKB_TREMBL</option> + <option value="WORMBASE" selected="true">WORMBASE</option> + <option value="ZFIN" selected="true">ZFIN</option> + <option value="description" selected="true">description</option> + <option value="domain_source" selected="true">domain_source</option> + <option value="id" selected="true">id</option> + <validator type="no_options" message="Please select at least one field" /> + </param> + <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> + <param name="query_field" type="select" label="Fields" > + <option value="AGRICOLA">AGRICOLA</option> + <option value="BIOSAMPLE">BIOSAMPLE</option> + <option value="DOI">DOI</option> + <option value="EC">EC</option> + <option value="EMBL">EMBL</option> + <option value="EMBLCDS">EMBLCDS</option> + <option value="EMBLCDS_version">EMBLCDS_version</option> + <option value="ENSEMBLGENOMES-GN">ENSEMBLGENOMES-GN</option> + <option value="ENSEMBLGENOMES-TR">ENSEMBLGENOMES-TR</option> + <option value="GOA">GOA</option> + <option value="H-INVDB">H-INVDB</option> + <option value="HGNC">HGNC</option> + <option value="IMGT_HLA">IMGT_HLA</option> + <option value="INTERPRO">INTERPRO</option> + <option value="MD5">MD5</option> + <option value="MGI">MGI</option> + <option value="PATENT_NUMBER">PATENT_NUMBER</option> + <option value="PDB">PDB</option> + <option value="PROJECT">PROJECT</option> + <option value="PUBMED">PUBMED</option> + <option value="SGD">SGD</option> + <option value="TAXON">TAXON</option> + <option value="UNIPROTKB_SWISS-PROT">UNIPROTKB_SWISS-PROT</option> + <option value="UNIPROTKB_TREMBL">UNIPROTKB_TREMBL</option> + <option value="WORMBASE">WORMBASE</option> + <option value="ZFIN">ZFIN</option> + <option value="bio_material">bio_material</option> + <option value="creation_date">creation_date</option> + <option value="culture_collection">culture_collection</option> + <option value="data_class">data_class</option> + <option value="description">description</option> + <option value="division">division</option> + <option value="domain_source">domain_source</option> + <option value="gene">gene</option> + <option value="gene_synonym">gene_synonym</option> + <option value="id">id</option> + <option value="keywords">keywords</option> + <option value="last_modification_date">last_modification_date</option> + <option value="length">length</option> + <option value="locus_tag">locus_tag</option> + <option value="molecule_type">molecule_type</option> + <option value="old_locus_tag">old_locus_tag</option> + <option value="organelle">organelle</option> + <option value="organism">organism</option> + <option value="organism_classification">organism_classification</option> + <option value="organism_species">organism_species</option> + <option value="product">product</option> + <option value="references">references</option> + <option value="sequence_version">sequence_version</option> + <option value="specimen_voucher">specimen_voucher</option> + <option value="topology">topology</option> + </param> + <conditional name="comp_operation"> + <param name="operation" type="select" label="Comparison operation" > + <option value="equal">equal</option> + <option value="not">not</option> + <option value="range">range</option> + </param> + <when value="equal"> + <param name="query_text" type="text" label="Searched term"/> + </when> + <when value="not"> + <param name="query_text" type="text" label="Searched term"/> + <param name="not_query_text" type="text" label="Limiting term"/> + </when> + <when value="range"> + <param name="min" type="text" label="From"/> + <param name="max" type="text" label="To"/> + </when> + </conditional> + </repeat> + </when> + + <when value="dgva"> + <param name="fields" type="select" label="Fields to extract" multiple="true"> + <option value="ENSEMBL" selected="true">ENSEMBL</option> + <option value="NCBI_TAXID" selected="true">NCBI_TAXID</option> + <option value="PUBMED" selected="true">PUBMED</option> + <option value="domain_source" selected="true">domain_source</option> + <option value="ftp_link" selected="true">ftp_link</option> + <option value="id" selected="true">id</option> + <option value="species" selected="true">species</option> + <option value="study_accession" selected="true">study_accession</option> + <option value="study_name" selected="true">study_name</option> + <option value="study_title" selected="true">study_title</option> + <option value="variant_count" selected="true">variant_count</option> + <option value="variant_placement" selected="true">variant_placement</option> + <option value="variant_sample" selected="true">variant_sample</option> + <option value="variant_type" selected="true">variant_type</option> + <option value="variation_level" selected="true">variation_level</option> + <validator type="no_options" message="Please select at least one field" /> + </param> + <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> + <param name="query_field" type="select" label="Fields" > + <option value="ENSEMBL">ENSEMBL</option> + <option value="NCBI_TAXID">NCBI_TAXID</option> + <option value="PUBMED">PUBMED</option> + <option value="domain_source">domain_source</option> + <option value="ftp_link">ftp_link</option> + <option value="id">id</option> + <option value="species">species</option> + <option value="study_accession">study_accession</option> + <option value="study_name">study_name</option> + <option value="study_title">study_title</option> + <option value="variant_count">variant_count</option> + <option value="variant_placement">variant_placement</option> + <option value="variant_sample">variant_sample</option> + <option value="variant_type">variant_type</option> + <option value="variation_level">variation_level</option> + </param> + <conditional name="comp_operation"> + <param name="operation" type="select" label="Comparison operation" > + <option value="equal">equal</option> + <option value="not">not</option> + <option value="range">range</option> + </param> + <when value="equal"> + <param name="query_text" type="text" label="Searched term"/> + </when> + <when value="not"> + <param name="query_text" type="text" label="Searched term"/> + <param name="not_query_text" type="text" label="Limiting term"/> + </when> + <when value="range"> + <param name="min" type="text" label="From"/> + <param name="max" type="text" label="To"/> + </when> + </conditional> + </repeat> + </when> + + <when value="atlas-genes-differential"> + <param name="fields" type="select" label="Fields to extract" multiple="true"> + <option value="ATLAS" selected="true">ATLAS</option> + <option value="EMBL" selected="true">EMBL</option> + <option value="ENSFAMILY" selected="true">ENSFAMILY</option> + <option value="ENSPROTEIN" selected="true">ENSPROTEIN</option> + <option value="ENTREZGENE" selected="true">ENTREZGENE</option> + <option value="GO" selected="true">GO</option> + <option value="INTERPRO" selected="true">INTERPRO</option> + <option value="REFSEQ" selected="true">REFSEQ</option> + <option value="UNIGENE" selected="true">UNIGENE</option> + <option value="UNIPROT" selected="true">UNIPROT</option> + <option value="description" selected="true">description</option> + <option value="domain_source" selected="true">domain_source</option> + <option value="id" selected="true">id</option> + <option value="name" selected="true">name</option> + <option value="organism_part" selected="true">organism_part</option> + <validator type="no_options" message="Please select at least one field" /> + </param> + <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> + <param name="query_field" type="select" label="Fields" > + <option value="ATLAS">ATLAS</option> + <option value="EMBL">EMBL</option> + <option value="ENSFAMILY">ENSFAMILY</option> + <option value="ENSPROTEIN">ENSPROTEIN</option> + <option value="ENSTRANSCRIPT">ENSTRANSCRIPT</option> + <option value="ENTREZGENE">ENTREZGENE</option> + <option value="GO">GO</option> + <option value="INTERPRO">INTERPRO</option> + <option value="REFSEQ">REFSEQ</option> + <option value="UNIGENE">UNIGENE</option> + <option value="UNIPROT">UNIPROT</option> + <option value="age">age</option> + <option value="biopsy_site">biopsy_site</option> + <option value="biotic_plant_treatment">biotic_plant_treatment</option> + <option value="block">block</option> + <option value="cell_cycle_stage">cell_cycle_stage</option> + <option value="cell_line">cell_line</option> + <option value="cell_type">cell_type</option> + <option value="cellular_component">cellular_component</option> + <option value="chromosomal_aberration">chromosomal_aberration</option> + <option value="clinical_history">clinical_history</option> + <option value="clinical_information">clinical_information</option> + <option value="clinical_treatment">clinical_treatment</option> + <option value="compound">compound</option> + <option value="cultivar">cultivar</option> + <option value="description">description</option> + <option value="developmental_stage">developmental_stage</option> + <option value="diet">diet</option> + <option value="disease">disease</option> + <option value="disease_staging">disease_staging</option> + <option value="disease_state">disease_state</option> + <option value="domain_source">domain_source</option> + <option value="ecotype">ecotype</option> + <option value="ensfamily_description">ensfamily_description</option> + <option value="environmental_history">environmental_history</option> + <option value="environmental_stress">environmental_stress</option> + <option value="estrogen_receptor_status">estrogen_receptor_status</option> + <option value="family_relationship">family_relationship</option> + <option value="fraction">fraction</option> + <option value="gene_biotype">gene_biotype</option> + <option value="generation">generation</option> + <option value="genetic_modification">genetic_modification</option> + <option value="genotype">genotype</option> + <option value="gestational_age">gestational_age</option> + <option value="goterm">goterm</option> + <option value="growth_condition">growth_condition</option> + <option value="hgnc_symbol">hgnc_symbol</option> + <option value="histology">histology</option> + <option value="id">id</option> + <option value="id_noversion">id_noversion</option> + <option value="individual">individual</option> + <option value="infect">infect</option> + <option value="injury">injury</option> + <option value="interproterm">interproterm</option> + <option value="irradiate">irradiate</option> + <option value="light">light</option> + <option value="material_type">material_type</option> + <option value="mirbase_accession">mirbase_accession</option> + <option value="mirbase_id">mirbase_id</option> + <option value="name">name</option> + <option value="organism_part">organism_part</option> + <option value="ortholog">ortholog</option> + <option value="passage">passage</option> + <option value="phenotype">phenotype</option> + <option value="physical_activity">physical_activity</option> + <option value="ploidy">ploidy</option> + <option value="population">population</option> + <option value="pregnancy">pregnancy</option> + <option value="protocol">protocol</option> + <option value="rna">rna</option> + <option value="rna_interference">rna_interference</option> + <option value="rnai">rnai</option> + <option value="sampling_site">sampling_site</option> + <option value="sampling_time">sampling_time</option> + <option value="sampling_time_point">sampling_time_point</option> + <option value="sex">sex</option> + <option value="specimen_with_known_storage_state">specimen_with_known_storage_state</option> + <option value="stimulus">stimulus</option> + <option value="strain">strain</option> + <option value="survival_time">survival_time</option> + <option value="synonym">synonym</option> + <option value="temperature">temperature</option> + <option value="time">time</option> + <option value="treatment">treatment</option> + <option value="tumor_grading">tumor_grading</option> + <option value="tumor_stage">tumor_stage</option> + </param> + <conditional name="comp_operation"> + <param name="operation" type="select" label="Comparison operation" > + <option value="equal">equal</option> + <option value="not">not</option> + <option value="range">range</option> + </param> + <when value="equal"> + <param name="query_text" type="text" label="Searched term"/> + </when> + <when value="not"> + <param name="query_text" type="text" label="Searched term"/> + <param name="not_query_text" type="text" label="Limiting term"/> + </when> + <when value="range"> + <param name="min" type="text" label="From"/> + <param name="max" type="text" label="To"/> + </when> + </conditional> + </repeat> + </when> + + <when value="efo"> + <param name="fields" type="select" label="Fields to extract" multiple="true"> + <option value="EFO" selected="true">EFO</option> + <option value="domain_source" selected="true">domain_source</option> + <option value="id" selected="true">id</option> + <option value="name" selected="true">name</option> + <validator type="no_options" message="Please select at least one field" /> + </param> + <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> + <param name="query_field" type="select" label="Fields" > + <option value="EFO">EFO</option> + <option value="domain_source">domain_source</option> + <option value="id">id</option> + <option value="name">name</option> + </param> + <conditional name="comp_operation"> + <param name="operation" type="select" label="Comparison operation" > + <option value="equal">equal</option> + <option value="not">not</option> + <option value="range">range</option> + </param> + <when value="equal"> + <param name="query_text" type="text" label="Searched term"/> + </when> + <when value="not"> + <param name="query_text" type="text" label="Searched term"/> + <param name="not_query_text" type="text" label="Limiting term"/> + </when> + <when value="range"> + <param name="min" type="text" label="From"/> + <param name="max" type="text" label="To"/> + </when> + </conditional> + </repeat> + </when> + + <when value="ega"> + <param name="fields" type="select" label="Fields to extract" multiple="true"> + <option value="EGA" selected="true">EGA</option> + <option value="PUBMED" selected="true">PUBMED</option> + <option value="TAXONOMY" selected="true">TAXONOMY</option> + <option value="description" selected="true">description</option> + <option value="domain_source" selected="true">domain_source</option> + <option value="full_dataset_link" selected="true">full_dataset_link</option> + <option value="id" selected="true">id</option> + <option value="name" selected="true">name</option> + <option value="omics_type" selected="true">omics_type</option> + <option value="technology_type" selected="true">technology_type</option> + <validator type="no_options" message="Please select at least one field" /> + </param> + <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> + <param name="query_field" type="select" label="Fields" > + <option value="EGA">EGA</option> + <option value="PUBMED">PUBMED</option> + <option value="TAXONOMY">TAXONOMY</option> + <option value="acc">acc</option> + <option value="acronym">acronym</option> + <option value="category">category</option> + <option value="contact_person">contact_person</option> + <option value="dataset_title">dataset_title</option> + <option value="description">description</option> + <option value="description_synonyms">description_synonyms</option> + <option value="domain_source">domain_source</option> + <option value="email">email</option> + <option value="full_dataset_link">full_dataset_link</option> + <option value="host">host</option> + <option value="host_link">host_link</option> + <option value="id">id</option> + <option value="name">name</option> + <option value="name_synonyms">name_synonyms</option> + <option value="omics_type">omics_type</option> + <option value="output_date">output_date</option> + <option value="pubmed_abstract">pubmed_abstract</option> + <option value="pubmed_abstract_synonyms">pubmed_abstract_synonyms</option> + <option value="pubmed_authors">pubmed_authors</option> + <option value="pubmed_title">pubmed_title</option> + <option value="pubmed_title_synonyms">pubmed_title_synonyms</option> + <option value="repository">repository</option> + <option value="source">source</option> + <option value="study_type">study_type</option> + <option value="technology_type">technology_type</option> + <option value="updated_date">updated_date</option> + <option value="url">url</option> + </param> + <conditional name="comp_operation"> + <param name="operation" type="select" label="Comparison operation" > + <option value="equal">equal</option> + <option value="not">not</option> + <option value="range">range</option> + </param> + <when value="equal"> + <param name="query_text" type="text" label="Searched term"/> + </when> + <when value="not"> + <param name="query_text" type="text" label="Searched term"/> + <param name="not_query_text" type="text" label="Limiting term"/> + </when> + <when value="range"> + <param name="min" type="text" label="From"/> + <param name="max" type="text" label="To"/> + </when> + </conditional> + </repeat> + </when> + + <when value="emdb"> + <param name="fields" type="select" label="Fields to extract" multiple="true"> + <option value="DOI" selected="true">DOI</option> + <option value="EMDB" selected="true">EMDB</option> + <option value="GO" selected="true">GO</option> + <option value="INTERPRO" selected="true">INTERPRO</option> + <option value="NCBI" selected="true">NCBI</option> + <option value="PDB" selected="true">PDB</option> + <option value="PUBMED" selected="true">PUBMED</option> + <option value="UNIPROT" selected="true">UNIPROT</option> + <option value="author" selected="true">author</option> + <option value="description" selected="true">description</option> + <option value="domain_source" selected="true">domain_source</option> + <option value="headerReleaseDate_date" selected="true">headerReleaseDate_date</option> + <option value="id" selected="true">id</option> + <option value="mapReleaseDate_date" selected="true">mapReleaseDate_date</option> + <option value="method" selected="true">method</option> + <option value="name" selected="true">name</option> + <option value="obsoletedDate_date" selected="true">obsoletedDate_date</option> + <option value="resolution" selected="true">resolution</option> + <option value="specimenstate" selected="true">specimenstate</option> + <validator type="no_options" message="Please select at least one field" /> + </param> + <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> + <param name="query_field" type="select" label="Fields" > + <option value="DOI">DOI</option> + <option value="EMDB">EMDB</option> + <option value="GO">GO</option> + <option value="INTERPRO">INTERPRO</option> + <option value="NCBI">NCBI</option> + <option value="PDB">PDB</option> + <option value="PUBMED">PUBMED</option> + <option value="UNIPROT">UNIPROT</option> + <option value="articletitle">articletitle</option> + <option value="author">author</option> + <option value="authorspublication">authorspublication</option> + <option value="book">book</option> + <option value="chaptertitle">chaptertitle</option> + <option value="depositionDate_date">depositionDate_date</option> + <option value="description">description</option> + <option value="domain_source">domain_source</option> + <option value="headerReleaseDate_date">headerReleaseDate_date</option> + <option value="id">id</option> + <option value="keywords">keywords</option> + <option value="lastUpdate_date">lastUpdate_date</option> + <option value="mapReleaseDate_date">mapReleaseDate_date</option> + <option value="method">method</option> + <option value="microscope">microscope</option> + <option value="name">name</option> + <option value="obsoletedDate_date">obsoletedDate_date</option> + <option value="resolution">resolution</option> + <option value="sciname">sciname</option> + <option value="scispeciesname">scispeciesname</option> + <option value="specimenstate">specimenstate</option> + <option value="synname">synname</option> + <option value="synspeciesname">synspeciesname</option> + <option value="thesistitle">thesistitle</option> + <option value="vitrificationinstrument">vitrificationinstrument</option> + </param> + <conditional name="comp_operation"> + <param name="operation" type="select" label="Comparison operation" > + <option value="equal">equal</option> + <option value="not">not</option> + <option value="range">range</option> + </param> + <when value="equal"> + <param name="query_text" type="text" label="Searched term"/> + </when> + <when value="not"> + <param name="query_text" type="text" label="Searched term"/> + <param name="not_query_text" type="text" label="Limiting term"/> + </when> + <when value="range"> + <param name="min" type="text" label="From"/> + <param name="max" type="text" label="To"/> + </when> + </conditional> + </repeat> + </when> + + <when value="epo"> + <param name="fields" type="select" label="Fields to extract" multiple="true"> + <option value="PATENT_NUMBER" selected="true">PATENT_NUMBER</option> + <option value="TAXON" selected="true">TAXON</option> + <option value="acc" selected="true">acc</option> + <option value="description" selected="true">description</option> + <option value="doc_file" selected="true">doc_file</option> + <option value="domain_source" selected="true">domain_source</option> + <option value="id" selected="true">id</option> + <option value="offset_end" selected="true">offset_end</option> + <option value="offset_start" selected="true">offset_start</option> + <validator type="no_options" message="Please select at least one field" /> + </param> + <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> + <param name="query_field" type="select" label="Fields" > + <option value="MD5">MD5</option> + <option value="PATENT_NUMBER">PATENT_NUMBER</option> + <option value="TAXON">TAXON</option> + <option value="acc">acc</option> + <option value="creation_date">creation_date</option> + <option value="data_class">data_class</option> + <option value="description">description</option> + <option value="division">division</option> + <option value="domain_source">domain_source</option> + <option value="id">id</option> + <option value="keywords">keywords</option> + <option value="last_modification_date">last_modification_date</option> + <option value="length">length</option> + <option value="molecule_type">molecule_type</option> + <option value="organelle">organelle</option> + <option value="organism">organism</option> + <option value="organism_classification">organism_classification</option> + <option value="organism_species">organism_species</option> + <option value="references">references</option> + <option value="sequence_version">sequence_version</option> + <option value="topology">topology</option> + </param> + <conditional name="comp_operation"> + <param name="operation" type="select" label="Comparison operation" > + <option value="equal">equal</option> + <option value="not">not</option> + <option value="range">range</option> + </param> + <when value="equal"> + <param name="query_text" type="text" label="Searched term"/> + </when> + <when value="not"> + <param name="query_text" type="text" label="Searched term"/> + <param name="not_query_text" type="text" label="Limiting term"/> + </when> + <when value="range"> + <param name="min" type="text" label="From"/> + <param name="max" type="text" label="To"/> + </when> + </conditional> + </repeat> + </when> + + <when value="elixir-registry"> + <param name="fields" type="select" label="Fields to extract" multiple="true"> + <option value="PMID" selected="true">PMID</option> + <option value="description" selected="true">description</option> + <option value="domain_source" selected="true">domain_source</option> + <option value="homepage" selected="true">homepage</option> + <option value="id" selected="true">id</option> + <option value="mirror" selected="true">mirror</option> + <option value="name" selected="true">name</option> + <option value="version" selected="true">version</option> + <validator type="no_options" message="Please select at least one field" /> + </param> + <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> + <param name="query_field" type="select" label="Fields" > + <option value="DOI">DOI</option> + <option value="PMID">PMID</option> + <option value="collection">collection</option> + <option value="cost">cost</option> + <option value="description">description</option> + <option value="domain_source">domain_source</option> + <option value="elixir_node">elixir_node</option> + <option value="elixir_status">elixir_status</option> + <option value="function_description">function_description</option> + <option value="function_name">function_name</option> + <option value="id">id</option> + <option value="id_noversion">id_noversion</option> + <option value="input_data_format">input_data_format</option> + <option value="input_data_type">input_data_type</option> + <option value="interface_type">interface_type</option> + <option value="language">language</option> + <option value="license">license</option> + <option value="name">name</option> + <option value="output_data_format">output_data_format</option> + <option value="output_data_type">output_data_type</option> + <option value="platform">platform</option> + <option value="resource_type">resource_type</option> + <option value="topic">topic</option> + <option value="version">version</option> + </param> + <conditional name="comp_operation"> + <param name="operation" type="select" label="Comparison operation" > + <option value="equal">equal</option> + <option value="not">not</option> + <option value="range">range</option> + </param> + <when value="equal"> + <param name="query_text" type="text" label="Searched term"/> + </when> + <when value="not"> + <param name="query_text" type="text" label="Searched term"/> + <param name="not_query_text" type="text" label="Limiting term"/> + </when> + <when value="range"> + <param name="min" type="text" label="From"/> + <param name="max" type="text" label="To"/> + </when> + </conditional> + </repeat> + </when> + + <when value="ensembl_gene"> + <param name="fields" type="select" label="Fields to extract" multiple="true"> + <option value="ARRAYEXPRESS" selected="true">ARRAYEXPRESS</option> + <option value="BIOGRID" selected="true">BIOGRID</option> + <option value="CCDS" selected="true">CCDS</option> + <option value="CINT_ANISEED_V1" selected="true">CINT_ANISEED_V1</option> + <option value="CINT_JGI_V1" selected="true">CINT_JGI_V1</option> + <option value="DBASS3" selected="true">DBASS3</option> + <option value="DBASS5" selected="true">DBASS5</option> + <option value="EC_NUMBER" selected="true">EC_NUMBER</option> + <option value="EMBL" selected="true">EMBL</option> + <option value="ENSEMBL" selected="true">ENSEMBL</option> + <option value="ENSEMBLGENOMES_ORTHOLOG" selected="true">ENSEMBLGENOMES_ORTHOLOG</option> + <option value="ENSEMBL_ORTHOLOG" selected="true">ENSEMBL_ORTHOLOG</option> + <option value="ENSG" selected="true">ENSG</option> + <option value="ENS_LRG_GENE" selected="true">ENS_LRG_GENE</option> + <option value="ENS_LRG_TRANSCRIPT" selected="true">ENS_LRG_TRANSCRIPT</option> + <option value="ENTREZGENE" selected="true">ENTREZGENE</option> + <option value="EPD" selected="true">EPD</option> + <option value="FLYBASECGID_GENE" selected="true">FLYBASECGID_GENE</option> + <option value="FLYBASECGID_TRANSCRIPT" selected="true">FLYBASECGID_TRANSCRIPT</option> + <option value="FLYBASENAME_GENE" selected="true">FLYBASENAME_GENE</option> + <option value="FLYBASENAME_TRANSCRIPT" selected="true">FLYBASENAME_TRANSCRIPT</option> + <option value="FLYBASENAME_TRANSLATION" selected="true">FLYBASENAME_TRANSLATION</option> + <option value="FLYBASE_ANNOTATION_ID" selected="true">FLYBASE_ANNOTATION_ID</option> + <option value="FLYBASE_GENE_ID" selected="true">FLYBASE_GENE_ID</option> + <option value="FLYBASE_TRANSCRIPT_ID" selected="true">FLYBASE_TRANSCRIPT_ID</option> + <option value="FLYBASE_TRANSLATION_ID" selected="true">FLYBASE_TRANSLATION_ID</option> + <option value="FLYREACTOME" selected="true">FLYREACTOME</option> + <option value="GENEDB" selected="true">GENEDB</option> + <option value="GENOMERNAI" selected="true">GENOMERNAI</option> + <option value="GO" selected="true">GO</option> + <option value="GOSLIM_GOA" selected="true">GOSLIM_GOA</option> + <option value="HGNC" selected="true">HGNC</option> + <option value="HPA" selected="true">HPA</option> + <option value="IMGT_GENE_DB" selected="true">IMGT_GENE_DB</option> + <option value="INTERACTIVEFLY" selected="true">INTERACTIVEFLY</option> + <option value="KEGG_ENZYME" selected="true">KEGG_ENZYME</option> + <option value="LRG" selected="true">LRG</option> + <option value="MEROPS" selected="true">MEROPS</option> + <option value="METACYC" selected="true">METACYC</option> + <option value="MGI" selected="true">MGI</option> + <option value="MIM_GENE" selected="true">MIM_GENE</option> + <option value="MIM_MORBID" selected="true">MIM_MORBID</option> + <option value="MIRBASE" selected="true">MIRBASE</option> + <option value="MITODROME" selected="true">MITODROME</option> + <option value="NCBI_TAXONOMY_ID" selected="true">NCBI_TAXONOMY_ID</option> + <option value="OXFORD_FGU_OA_GENE" selected="true">OXFORD_FGU_OA_GENE</option> + <option value="OXFORD_FGU_OA_TSCRIPT" selected="true">OXFORD_FGU_OA_TSCRIPT</option> + <option value="PDB" selected="true">PDB</option> + <option value="PLATYPUS_OLFACTORY_RECEPTOR" selected="true">PLATYPUS_OLFACTORY_RECEPTOR</option> + <option value="PROTEIN_ID" selected="true">PROTEIN_ID</option> + <option value="PUBMED" selected="true">PUBMED</option> + <option value="REACTOME" selected="true">REACTOME</option> + <option value="REACTOME_GENE" selected="true">REACTOME_GENE</option> + <option value="REACTOME_TRANSCRIPT" selected="true">REACTOME_TRANSCRIPT</option> + <option value="REFSEQ_DNA" selected="true">REFSEQ_DNA</option> + <option value="REFSEQ_DNA_PREDICTED" selected="true">REFSEQ_DNA_PREDICTED</option> + <option value="REFSEQ_MRNA" selected="true">REFSEQ_MRNA</option> + <option value="REFSEQ_MRNA_PREDICTED" selected="true">REFSEQ_MRNA_PREDICTED</option> + <option value="REFSEQ_NCRNA" selected="true">REFSEQ_NCRNA</option> + <option value="REFSEQ_NCRNA_PREDICTED" selected="true">REFSEQ_NCRNA_PREDICTED</option> + <option value="REFSEQ_PEPTIDE" selected="true">REFSEQ_PEPTIDE</option> + <option value="REFSEQ_PEPTIDE_PREDICTED" selected="true">REFSEQ_PEPTIDE_PREDICTED</option> + <option value="REFSEQ_RNA" selected="true">REFSEQ_RNA</option> + <option value="REFSEQ_RNA_PREDICTED" selected="true">REFSEQ_RNA_PREDICTED</option> + <option value="RFAM" selected="true">RFAM</option> + <option value="RGD" selected="true">RGD</option> + <option value="RNACENTRAL" selected="true">RNACENTRAL</option> + <option value="SHARES_CDS_AND_UTR_WITH_OTTT" selected="true">SHARES_CDS_AND_UTR_WITH_OTTT</option> + <option value="SHARES_CDS_WITH_OTTT" selected="true">SHARES_CDS_WITH_OTTT</option> + <option value="TRANSFAC" selected="true">TRANSFAC</option> + <option value="UCSC" selected="true">UCSC</option> + <option value="UNIGENE" selected="true">UNIGENE</option> + <option value="UNIPARC" selected="true">UNIPARC</option> + <option value="UNIPATHWAY" selected="true">UNIPATHWAY</option> + <option value="UNIPROT" selected="true">UNIPROT</option> + <option value="VEGA_GENE" selected="true">VEGA_GENE</option> + <option value="VEGA_TRANSCRIPT" selected="true">VEGA_TRANSCRIPT</option> + <option value="VEGA_TRANSLATION" selected="true">VEGA_TRANSLATION</option> + <option value="VGNC" selected="true">VGNC</option> + <option value="WIKIGENE" selected="true">WIKIGENE</option> + <option value="WORMBASE_GENE" selected="true">WORMBASE_GENE</option> + <option value="WORMBASE_GSEQNAME" selected="true">WORMBASE_GSEQNAME</option> + <option value="WORMBASE_LOCUS" selected="true">WORMBASE_LOCUS</option> + <option value="WORMBASE_TRANSCRIPT" selected="true">WORMBASE_TRANSCRIPT</option> + <option value="WORMPEP_ID" selected="true">WORMPEP_ID</option> + <option value="XENBASE" selected="true">XENBASE</option> + <option value="ZFIN_ID" selected="true">ZFIN_ID</option> + <option value="ZFIN_XPAT" selected="true">ZFIN_XPAT</option> + <option value="description" selected="true">description</option> + <option value="domain_source" selected="true">domain_source</option> + <option value="exon" selected="true">exon</option> + <option value="exon_count" selected="true">exon_count</option> + <option value="featuretype" selected="true">featuretype</option> + <option value="gene_name" selected="true">gene_name</option> + <option value="gene_synonym" selected="true">gene_synonym</option> + <option value="id" selected="true">id</option> + <option value="name" selected="true">name</option> + <option value="peptide" selected="true">peptide</option> + <option value="source" selected="true">source</option> + <option value="species" selected="true">species</option> + <option value="system_name" selected="true">system_name</option> + <option value="transcript" selected="true">transcript</option> + <option value="transcript_count" selected="true">transcript_count</option> + <validator type="no_options" message="Please select at least one field" /> + </param> + <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> + <param name="query_field" type="select" label="Fields" > + <option value="ARRAYEXPRESS">ARRAYEXPRESS</option> + <option value="BIOGRID">BIOGRID</option> + <option value="CCDS">CCDS</option> + <option value="CINT_ANISEED_V1">CINT_ANISEED_V1</option> + <option value="CINT_JGI_V1">CINT_JGI_V1</option> + <option value="CLONE_BASED_ENSEMBL_GENE">CLONE_BASED_ENSEMBL_GENE</option> + <option value="CLONE_BASED_ENSEMBL_TRANSCRIPT">CLONE_BASED_ENSEMBL_TRANSCRIPT</option> + <option value="CLONE_BASED_VEGA_GENE">CLONE_BASED_VEGA_GENE</option> + <option value="CLONE_BASED_VEGA_TRANSCRIPT">CLONE_BASED_VEGA_TRANSCRIPT</option> + <option value="DBASS3">DBASS3</option> + <option value="DBASS5">DBASS5</option> + <option value="EC_NUMBER">EC_NUMBER</option> + <option value="EMBL">EMBL</option> + <option value="ENSEMBL">ENSEMBL</option> + <option value="ENSEMBLGENOMES_ORTHOLOG">ENSEMBLGENOMES_ORTHOLOG</option> + <option value="ENSEMBLVARIATION">ENSEMBLVARIATION</option> + <option value="ENSEMBL_ORTHOLOG">ENSEMBL_ORTHOLOG</option> + <option value="ENSG">ENSG</option> + <option value="ENSP_IDENT">ENSP_IDENT</option> + <option value="ENST_CDS">ENST_CDS</option> + <option value="ENST_IDENT">ENST_IDENT</option> + <option value="ENS_LRG_GENE">ENS_LRG_GENE</option> + <option value="ENS_LRG_TRANSCRIPT">ENS_LRG_TRANSCRIPT</option> + <option value="ENTREZGENE">ENTREZGENE</option> + <option value="ENTREZGENE_TRANS_NAME">ENTREZGENE_TRANS_NAME</option> + <option value="EPD">EPD</option> + <option value="FLYBASECGID_GENE">FLYBASECGID_GENE</option> + <option value="FLYBASECGID_TRANSCRIPT">FLYBASECGID_TRANSCRIPT</option> + <option value="FLYBASECGID_TRANSLATION">FLYBASECGID_TRANSLATION</option> + <option value="FLYBASENAME_GENE">FLYBASENAME_GENE</option> + <option value="FLYBASENAME_TRANSCRIPT">FLYBASENAME_TRANSCRIPT</option> + <option value="FLYBASENAME_TRANSLATION">FLYBASENAME_TRANSLATION</option> + <option value="FLYBASE_ANNOTATION_ID">FLYBASE_ANNOTATION_ID</option> + <option value="FLYBASE_GENE_ID">FLYBASE_GENE_ID</option> + <option value="FLYBASE_TRANSCRIPT_ID">FLYBASE_TRANSCRIPT_ID</option> + <option value="FLYBASE_TRANSLATION_ID">FLYBASE_TRANSLATION_ID</option> + <option value="FLYREACTOME">FLYREACTOME</option> + <option value="GENEDB">GENEDB</option> + <option value="GENOMERNAI">GENOMERNAI</option> + <option value="GO">GO</option> + <option value="GOSLIM_GOA">GOSLIM_GOA</option> + <option value="HGNC">HGNC</option> + <option value="HGNC_TRANS_NAME">HGNC_TRANS_NAME</option> + <option value="HPA">HPA</option> + <option value="IMGT_GENE_DB">IMGT_GENE_DB</option> + <option value="IMGT_HLA">IMGT_HLA</option> + <option value="INTERACTIVEFLY">INTERACTIVEFLY</option> + <option value="KEGG_ENZYME">KEGG_ENZYME</option> + <option value="LRG">LRG</option> + <option value="MEROPS">MEROPS</option> + <option value="METACYC">METACYC</option> + <option value="MGI">MGI</option> + <option value="MGI_TRANS_NAME">MGI_TRANS_NAME</option> + <option value="MIM_GENE">MIM_GENE</option> + <option value="MIM_MORBID">MIM_MORBID</option> + <option value="MIRBASE">MIRBASE</option> + <option value="MIRBASE_TRANS_NAME">MIRBASE_TRANS_NAME</option> + <option value="MITODROME">MITODROME</option> + <option value="NCBI_TAXONOMY_ID">NCBI_TAXONOMY_ID</option> + <option value="OTTG">OTTG</option> + <option value="OTTP">OTTP</option> + <option value="OTTT">OTTT</option> + <option value="OXFORD_FGU_OA_GENE">OXFORD_FGU_OA_GENE</option> + <option value="OXFORD_FGU_OA_TSCRIPT">OXFORD_FGU_OA_TSCRIPT</option> + <option value="PDB">PDB</option> + <option value="PLATYPUS_OLFACTORY_RECEPTOR">PLATYPUS_OLFACTORY_RECEPTOR</option> + <option value="PROTEIN_ID">PROTEIN_ID</option> + <option value="PUBMED">PUBMED</option> + <option value="QUICK_GO">QUICK_GO</option> + <option value="REACTOME">REACTOME</option> + <option value="REACTOME_GENE">REACTOME_GENE</option> + <option value="REACTOME_TRANSCRIPT">REACTOME_TRANSCRIPT</option> + <option value="REFSEQ_DNA">REFSEQ_DNA</option> + <option value="REFSEQ_DNA_PREDICTED">REFSEQ_DNA_PREDICTED</option> + <option value="REFSEQ_GENOMIC">REFSEQ_GENOMIC</option> + <option value="REFSEQ_MRNA">REFSEQ_MRNA</option> + <option value="REFSEQ_MRNA_PREDICTED">REFSEQ_MRNA_PREDICTED</option> + <option value="REFSEQ_NCRNA">REFSEQ_NCRNA</option> + <option value="REFSEQ_NCRNA_PREDICTED">REFSEQ_NCRNA_PREDICTED</option> + <option value="REFSEQ_PEPTIDE">REFSEQ_PEPTIDE</option> + <option value="REFSEQ_PEPTIDE_PREDICTED">REFSEQ_PEPTIDE_PREDICTED</option> + <option value="REFSEQ_RNA">REFSEQ_RNA</option> + <option value="REFSEQ_RNA_PREDICTED">REFSEQ_RNA_PREDICTED</option> + <option value="RFAM">RFAM</option> + <option value="RFAM_TRANS_NAME">RFAM_TRANS_NAME</option> + <option value="RGD">RGD</option> + <option value="RGD_TRANS_NAME">RGD_TRANS_NAME</option> + <option value="RNACENTRAL">RNACENTRAL</option> + <option value="SGD_GENE">SGD_GENE</option> + <option value="SGD_TRANSCRIPT">SGD_TRANSCRIPT</option> + <option value="SHARES_CDS_AND_UTR_WITH_OTTT">SHARES_CDS_AND_UTR_WITH_OTTT</option> + <option value="SHARES_CDS_WITH_OTTT">SHARES_CDS_WITH_OTTT</option> + <option value="TRANSFAC">TRANSFAC</option> + <option value="UCSC">UCSC</option> + <option value="UNIGENE">UNIGENE</option> + <option value="UNIPARC">UNIPARC</option> + <option value="UNIPATHWAY">UNIPATHWAY</option> + <option value="UNIPROT">UNIPROT</option> + <option value="VEGA_GENE">VEGA_GENE</option> + <option value="VEGA_TRANSCRIPT">VEGA_TRANSCRIPT</option> + <option value="VEGA_TRANSLATION">VEGA_TRANSLATION</option> + <option value="VGNC">VGNC</option> + <option value="VGNC_TRANS_NAME">VGNC_TRANS_NAME</option> + <option value="WIKIGENE">WIKIGENE</option> + <option value="WORMBASE_GENE">WORMBASE_GENE</option> + <option value="WORMBASE_GSEQNAME">WORMBASE_GSEQNAME</option> + <option value="WORMBASE_LOCUS">WORMBASE_LOCUS</option> + <option value="WORMBASE_TRANSCRIPT">WORMBASE_TRANSCRIPT</option> + <option value="WORMPEP_ID">WORMPEP_ID</option> + <option value="XENBASE">XENBASE</option> + <option value="XENBASE_TRANS_NAME">XENBASE_TRANS_NAME</option> + <option value="ZFIN_ID">ZFIN_ID</option> + <option value="ZFIN_ID_TRANS_NAME">ZFIN_ID_TRANS_NAME</option> + <option value="ZFIN_XPAT">ZFIN_XPAT</option> + <option value="alt_allele">alt_allele</option> + <option value="dbass3_synonym">dbass3_synonym</option> + <option value="dbass5_synonym">dbass5_synonym</option> + <option value="description">description</option> + <option value="domain_source">domain_source</option> + <option value="entrezgene_synonym">entrezgene_synonym</option> + <option value="exon">exon</option> + <option value="flybase_gene_id_synonym">flybase_gene_id_synonym</option> + <option value="flybase_transcript_id_synonym">flybase_transcript_id_synonym</option> + <option value="flybase_translation_id_synonym">flybase_translation_id_synonym</option> + <option value="gene_name">gene_name</option> + <option value="gene_synonym">gene_synonym</option> + <option value="haplotype">haplotype</option> + <option value="hgnc_synonym">hgnc_synonym</option> + <option value="id">id</option> + <option value="mgi_synonym">mgi_synonym</option> + <option value="mim_gene_synonym">mim_gene_synonym</option> + <option value="mim_morbid_synonym">mim_morbid_synonym</option> + <option value="name">name</option> + <option value="peptide">peptide</option> + <option value="rgd_synonym">rgd_synonym</option> + <option value="sgd_gene_synonym">sgd_gene_synonym</option> + <option value="source">source</option> + <option value="species">species</option> + <option value="system_name">system_name</option> + <option value="transcript">transcript</option> + <option value="uniprot_synonym">uniprot_synonym</option> + <option value="zfin_id_synonym">zfin_id_synonym</option> + </param> + <conditional name="comp_operation"> + <param name="operation" type="select" label="Comparison operation" > + <option value="equal">equal</option> + <option value="not">not</option> + <option value="range">range</option> + </param> + <when value="equal"> + <param name="query_text" type="text" label="Searched term"/> + </when> + <when value="not"> + <param name="query_text" type="text" label="Searched term"/> + <param name="not_query_text" type="text" label="Limiting term"/> + </when> + <when value="range"> + <param name="min" type="text" label="From"/> + <param name="max" type="text" label="To"/> + </when> + </conditional> + </repeat> + </when> + + <when value="ensemblGenomes_gene"> + <param name="fields" type="select" label="Fields to extract" multiple="true"> + <option value="AGD_GENE" selected="true">AGD_GENE</option> + <option value="AGD_TRANSCRIPT" selected="true">AGD_TRANSCRIPT</option> + <option value="ANT_GENOMES_PORTAL" selected="true">ANT_GENOMES_PORTAL</option> + <option value="ARRAYEXPRESS" selected="true">ARRAYEXPRESS</option> + <option value="BINDINGDB" selected="true">BINDINGDB</option> + <option value="BIOCYC" selected="true">BIOCYC</option> + <option value="BIOGRID" selected="true">BIOGRID</option> + <option value="BRENDA" selected="true">BRENDA</option> + <option value="BROAD_MAGNAPORTHE_DB" selected="true">BROAD_MAGNAPORTHE_DB</option> + <option value="BROAD_P_NODORUM_GENE" selected="true">BROAD_P_NODORUM_GENE</option> + <option value="CADRE_AFUM_A1163" selected="true">CADRE_AFUM_A1163</option> + <option value="DIP" selected="true">DIP</option> + <option value="DISPROT" selected="true">DISPROT</option> + <option value="DRUGBANK" selected="true">DRUGBANK</option> + <option value="ECHOBASE" selected="true">ECHOBASE</option> + <option value="ECOGENE" selected="true">ECOGENE</option> + <option value="EC_NUMBER" selected="true">EC_NUMBER</option> + <option value="EMBL" selected="true">EMBL</option> + <option value="ENSEMBL" selected="true">ENSEMBL</option> + <option value="ENTREZGENE" selected="true">ENTREZGENE</option> + <option value="EPD" selected="true">EPD</option> + <option value="FGDB" selected="true">FGDB</option> + <option value="FLYBASECGID_GENE" selected="true">FLYBASECGID_GENE</option> + <option value="FLYBASECGID_TRANSCRIPT" selected="true">FLYBASECGID_TRANSCRIPT</option> + <option value="FLYBASENAME_GENE" selected="true">FLYBASENAME_GENE</option> + <option value="FLYBASENAME_TRANSCRIPT" selected="true">FLYBASENAME_TRANSCRIPT</option> + <option value="FLYBASENAME_TRANSLATION" selected="true">FLYBASENAME_TRANSLATION</option> + <option value="FLYBASE_ANNOTATION_ID" selected="true">FLYBASE_ANNOTATION_ID</option> + <option value="FLYBASE_GENE_ID" selected="true">FLYBASE_GENE_ID</option> + <option value="FLYBASE_TRANSCRIPT_ID" selected="true">FLYBASE_TRANSCRIPT_ID</option> + <option value="FLYBASE_TRANSLATION_ID" selected="true">FLYBASE_TRANSLATION_ID</option> + <option value="FLYREACTOME" selected="true">FLYREACTOME</option> + <option value="GENBANK" selected="true">GENBANK</option> + <option value="GENEDB" selected="true">GENEDB</option> + <option value="GENEID" selected="true">GENEID</option> + <option value="GENOMERNAI" selected="true">GENOMERNAI</option> + <option value="GFBGP" selected="true">GFBGP</option> + <option value="GO" selected="true">GO</option> + <option value="GOA" selected="true">GOA</option> + <option value="GRAMENE_PLANT_REACTOME" selected="true">GRAMENE_PLANT_REACTOME</option> + <option value="HSSP" selected="true">HSSP</option> + <option value="IMMUNODB" selected="true">IMMUNODB</option> + <option value="INTACT" selected="true">INTACT</option> + <option value="INTENZ" selected="true">INTENZ</option> + <option value="INTERPRO" selected="true">INTERPRO</option> + <option value="KEGG" selected="true">KEGG</option> + <option value="KEGG_ENZYME" selected="true">KEGG_ENZYME</option> + <option value="LEGIOLIST" selected="true">LEGIOLIST</option> + <option value="MEROPS" selected="true">MEROPS</option> + <option value="METACYC" selected="true">METACYC</option> + <option value="MGP" selected="true">MGP</option> + <option value="MINT" selected="true">MINT</option> + <option value="MIRBASE" selected="true">MIRBASE</option> + <option value="MIRBASE_GENE_NAME" selected="true">MIRBASE_GENE_NAME</option> + <option value="MIRBASE_TRANS_NAME" selected="true">MIRBASE_TRANS_NAME</option> + <option value="MITODROME" selected="true">MITODROME</option> + <option value="MTGD" selected="true">MTGD</option> + <option value="MYCGR3_JGI_V2.0_GENE" selected="true">MYCGR3_JGI_V2.0_GENE</option> + <option value="NCBI_TAXONOMY_ID" selected="true">NCBI_TAXONOMY_ID</option> + <option value="NECHA_JGI_V2.0" selected="true">NECHA_JGI_V2.0</option> + <option value="NHPRTR" selected="true">NHPRTR</option> + <option value="PBO" selected="true">PBO</option> + <option value="PDB" selected="true">PDB</option> + <option value="PDBSUM" selected="true">PDBSUM</option> + <option value="PEROXIBASE" selected="true">PEROXIBASE</option> + <option value="PGD_GENE" selected="true">PGD_GENE</option> + <option value="PGSC_GENE" selected="true">PGSC_GENE</option> + <option value="PIR" selected="true">PIR</option> + <option value="POMBASE_GENE_NAME" selected="true">POMBASE_GENE_NAME</option> + <option value="POMBASE_TRANSCRIPT" selected="true">POMBASE_TRANSCRIPT</option> + <option value="PRIDE" selected="true">PRIDE</option> + <option value="PROTEIN_ID" selected="true">PROTEIN_ID</option> + <option value="PROTEIN_ID_PREDICTED" selected="true">PROTEIN_ID_PREDICTED</option> + <option value="PSEUDOCAP" selected="true">PSEUDOCAP</option> + <option value="PUBMED" selected="true">PUBMED</option> + <option value="PUBMED_POMBASE" selected="true">PUBMED_POMBASE</option> + <option value="REACTOME" selected="true">REACTOME</option> + <option value="REBASE" selected="true">REBASE</option> + <option value="REFSEQ" selected="true">REFSEQ</option> + <option value="REFSEQ_DNA" selected="true">REFSEQ_DNA</option> + <option value="REFSEQ_DNA_PREDICTED" selected="true">REFSEQ_DNA_PREDICTED</option> + <option value="REFSEQ_MRNA" selected="true">REFSEQ_MRNA</option> + <option value="REFSEQ_MRNA_PREDICTED" selected="true">REFSEQ_MRNA_PREDICTED</option> + <option value="REFSEQ_NCRNA" selected="true">REFSEQ_NCRNA</option> + <option value="REFSEQ_NCRNA_PREDICTED" selected="true">REFSEQ_NCRNA_PREDICTED</option> + <option value="REFSEQ_PEPTIDE" selected="true">REFSEQ_PEPTIDE</option> + <option value="REFSEQ_PEPTIDE_PREDICTED" selected="true">REFSEQ_PEPTIDE_PREDICTED</option> + <option value="RFAM" selected="true">RFAM</option> + <option value="RFAM_GENE" selected="true">RFAM_GENE</option> + <option value="RHEA" selected="true">RHEA</option> + <option value="RIBOSOMAL_PROTEIN_GENE_DATABASE" selected="true">RIBOSOMAL_PROTEIN_GENE_DATABASE</option> + <option value="SCHISTODB" selected="true">SCHISTODB</option> + <option value="SGD" selected="true">SGD</option> + <option value="SO" selected="true">SO</option> + <option value="SPBASE" selected="true">SPBASE</option> + <option value="SPD" selected="true">SPD</option> + <option value="STRING" selected="true">STRING</option> + <option value="SUBTILIST" selected="true">SUBTILIST</option> + <option value="SWISS_MODEL" selected="true">SWISS_MODEL</option> + <option value="TAIR_SYMBOL" selected="true">TAIR_SYMBOL</option> + <option value="TRANSFAC" selected="true">TRANSFAC</option> + <option value="TUBERCULIST" selected="true">TUBERCULIST</option> + <option value="TUBER_GENOSCOPE_GENE" selected="true">TUBER_GENOSCOPE_GENE</option> + <option value="UNIGENE" selected="true">UNIGENE</option> + <option value="UNIPARC" selected="true">UNIPARC</option> + <option value="UNIPATHWAY" selected="true">UNIPATHWAY</option> + <option value="UNIPROT" selected="true">UNIPROT</option> + <option value="VB_COMMUNITY_ANNOTATION" selected="true">VB_COMMUNITY_ANNOTATION</option> + <option value="VB_EXTERNAL_DESCRIPTION" selected="true">VB_EXTERNAL_DESCRIPTION</option> + <option value="VB_RNA_DESCRIPTION" selected="true">VB_RNA_DESCRIPTION</option> + <option value="WIKIGENE" selected="true">WIKIGENE</option> + <option value="WORMBASE_GENE" selected="true">WORMBASE_GENE</option> + <option value="WORMBASE_GSEQNAME" selected="true">WORMBASE_GSEQNAME</option> + <option value="WORMBASE_LOCUS" selected="true">WORMBASE_LOCUS</option> + <option value="WORMBASE_TRANSCRIPT" selected="true">WORMBASE_TRANSCRIPT</option> + <option value="WORMPEP_ID" selected="true">WORMPEP_ID</option> + <option value="ZNGP" selected="true">ZNGP</option> + <option value="collection" selected="true">collection</option> + <option value="database" selected="true">database</option> + <option value="description" selected="true">description</option> + <option value="domain_source" selected="true">domain_source</option> + <option value="exon" selected="true">exon</option> + <option value="exon_count" selected="true">exon_count</option> + <option value="featuretype" selected="true">featuretype</option> + <option value="gene_name" selected="true">gene_name</option> + <option value="gene_synonym" selected="true">gene_synonym</option> + <option value="genetree" selected="true">genetree</option> + <option value="genomic_unit" selected="true">genomic_unit</option> + <option value="id" selected="true">id</option> + <option value="location" selected="true">location</option> + <option value="name" selected="true">name</option> + <option value="peptide" selected="true">peptide</option> + <option value="source" selected="true">source</option> + <option value="species" selected="true">species</option> + <option value="system_name" selected="true">system_name</option> + <option value="transcript" selected="true">transcript</option> + <option value="transcript_count" selected="true">transcript_count</option> + <validator type="no_options" message="Please select at least one field" /> + </param> + <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> + <param name="query_field" type="select" label="Fields" > + <option value="AGD_GENE">AGD_GENE</option> + <option value="AGD_TRANSCRIPT">AGD_TRANSCRIPT</option> + <option value="AGI_GENE">AGI_GENE</option> + <option value="AGI_TRANSCRIPT">AGI_TRANSCRIPT</option> + <option value="ANT_GENOMES_PORTAL">ANT_GENOMES_PORTAL</option> + <option value="ARRAYEXPRESS">ARRAYEXPRESS</option> + <option value="ASPGD_GENE">ASPGD_GENE</option> + <option value="ASPGD_TRANSCRIPT">ASPGD_TRANSCRIPT</option> + <option value="BAYLORCOLLEGE">BAYLORCOLLEGE</option> + <option value="BGI_EST_CLUSTER">BGI_EST_CLUSTER</option> + <option value="BGI_GENE">BGI_GENE</option> + <option value="BINDINGDB">BINDINGDB</option> + <option value="BIOCYC">BIOCYC</option> + <option value="BIOGRID">BIOGRID</option> + <option value="BRAD_TRANSCRIPT">BRAD_TRANSCRIPT</option> + <option value="BRENDA">BRENDA</option> + <option value="BROAD_F_OXYSPORUM">BROAD_F_OXYSPORUM</option> + <option value="BROAD_G_MONILIFORMIS">BROAD_G_MONILIFORMIS</option> + <option value="BROAD_G_ZEAE">BROAD_G_ZEAE</option> + <option value="BROAD_MAGNAPORTHE_DB">BROAD_MAGNAPORTHE_DB</option> + <option value="BROAD_M_VIOLACEUM">BROAD_M_VIOLACEUM</option> + <option value="BROAD_P_INFESTANS">BROAD_P_INFESTANS</option> + <option value="BROAD_P_NODORUM_GENE">BROAD_P_NODORUM_GENE</option> + <option value="BROAD_P_TRITICINA">BROAD_P_TRITICINA</option> + <option value="CADRE">CADRE</option> + <option value="CADRE_AFUM_A1163">CADRE_AFUM_A1163</option> + <option value="CADRE_GENE">CADRE_GENE</option> + <option value="CADRE_TRANSCRIPT">CADRE_TRANSCRIPT</option> + <option value="CELERA_GENE">CELERA_GENE</option> + <option value="CELERA_PEP">CELERA_PEP</option> + <option value="CELERA_TRANS">CELERA_TRANS</option> + <option value="DIP">DIP</option> + <option value="DISPROT">DISPROT</option> + <option value="DRUGBANK">DRUGBANK</option> + <option value="ECHOBASE">ECHOBASE</option> + <option value="ECOGENE">ECOGENE</option> + <option value="EC_NUMBER">EC_NUMBER</option> + <option value="EMBL">EMBL</option> + <option value="ENA_FEATURE_GENE">ENA_FEATURE_GENE</option> + <option value="ENA_FEATURE_PROTEIN">ENA_FEATURE_PROTEIN</option> + <option value="ENA_FEATURE_TRANSCRIPT">ENA_FEATURE_TRANSCRIPT</option> + <option value="ENA_GENE">ENA_GENE</option> + <option value="ENA_TRANSCRIPT">ENA_TRANSCRIPT</option> + <option value="ENSEMBL">ENSEMBL</option> + <option value="ENTREZGENE">ENTREZGENE</option> + <option value="EPD">EPD</option> + <option value="FGDB">FGDB</option> + <option value="FLYBASECGID_GENE">FLYBASECGID_GENE</option> + <option value="FLYBASECGID_TRANSCRIPT">FLYBASECGID_TRANSCRIPT</option> + <option value="FLYBASECGID_TRANSLATION">FLYBASECGID_TRANSLATION</option> + <option value="FLYBASENAME_GENE">FLYBASENAME_GENE</option> + <option value="FLYBASENAME_TRANSCRIPT">FLYBASENAME_TRANSCRIPT</option> + <option value="FLYBASENAME_TRANSLATION">FLYBASENAME_TRANSLATION</option> + <option value="FLYBASE_ANNOTATION_ID">FLYBASE_ANNOTATION_ID</option> + <option value="FLYBASE_GENE_ID">FLYBASE_GENE_ID</option> + <option value="FLYBASE_TRANSCRIPT_ID">FLYBASE_TRANSCRIPT_ID</option> + <option value="FLYBASE_TRANSLATION_ID">FLYBASE_TRANSLATION_ID</option> + <option value="FLYREACTOME">FLYREACTOME</option> + <option value="FSTS">FSTS</option> + <option value="FYPO">FYPO</option> + <option value="GENBANK">GENBANK</option> + <option value="GENEDB">GENEDB</option> + <option value="GENEID">GENEID</option> + <option value="GENEINDEX">GENEINDEX</option> + <option value="GENOMERNAI">GENOMERNAI</option> + <option value="GFBGP">GFBGP</option> + <option value="GO">GO</option> + <option value="GOA">GOA</option> + <option value="GRAMENE_MARKERSDB_EST">GRAMENE_MARKERSDB_EST</option> + <option value="GRAMENE_MARKERSDB_MRNA">GRAMENE_MARKERSDB_MRNA</option> + <option value="GRAMENE_PLANT_REACTOME">GRAMENE_PLANT_REACTOME</option> + <option value="HSSP">HSSP</option> + <option value="IBSC">IBSC</option> + <option value="IMMUNODB">IMMUNODB</option> + <option value="INTACT">INTACT</option> + <option value="INTENZ">INTENZ</option> + <option value="INTERACTIVEFLY">INTERACTIVEFLY</option> + <option value="INTERPRO">INTERPRO</option> + <option value="JGI_GENE">JGI_GENE</option> + <option value="JGI_TRANSCRIPT">JGI_TRANSCRIPT</option> + <option value="KEGG">KEGG</option> + <option value="KEGG_ENZYME">KEGG_ENZYME</option> + <option value="LEGIOLIST">LEGIOLIST</option> + <option value="LGBPRATT_EST_CLUSTER">LGBPRATT_EST_CLUSTER</option> + <option value="LNCC">LNCC</option> + <option value="MEROPS">MEROPS</option> + <option value="METACYC">METACYC</option> + <option value="MGP">MGP</option> + <option value="MINT">MINT</option> + <option value="MIRBASE">MIRBASE</option> + <option value="MIRBASE_GENE_NAME">MIRBASE_GENE_NAME</option> + <option value="MIRBASE_TRANS_NAME">MIRBASE_TRANS_NAME</option> + <option value="MITODROME">MITODROME</option> + <option value="MOD">MOD</option> + <option value="MTGD">MTGD</option> + <option value="MYCGR3_JGI_V2.0_GENE">MYCGR3_JGI_V2.0_GENE</option> + <option value="NCBI_TAXONOMY_ID">NCBI_TAXONOMY_ID</option> + <option value="NECHA_JGI_V2.0">NECHA_JGI_V2.0</option> + <option value="NHPRTR">NHPRTR</option> + <option value="PBO">PBO</option> + <option value="PDB">PDB</option> + <option value="PDBSUM">PDBSUM</option> + <option value="PEROXIBASE">PEROXIBASE</option> + <option value="PGD_GENE">PGD_GENE</option> + <option value="PGSC_GENE">PGSC_GENE</option> + <option value="PHI">PHI</option> + <option value="PHYRA_JGI_V1.1">PHYRA_JGI_V1.1</option> + <option value="PIR">PIR</option> + <option value="PLANTGDB_PUT">PLANTGDB_PUT</option> + <option value="PO">PO</option> + <option value="POMBASE_GENE_NAME">POMBASE_GENE_NAME</option> + <option value="POMBASE_ORTHOLOG">POMBASE_ORTHOLOG</option> + <option value="POMBASE_TRANSCRIPT">POMBASE_TRANSCRIPT</option> + <option value="POMBASE_TRANSLATION">POMBASE_TRANSLATION</option> + <option value="PRIDE">PRIDE</option> + <option value="PROTEIN_ID">PROTEIN_ID</option> + <option value="PROTEIN_ID_PREDICTED">PROTEIN_ID_PREDICTED</option> + <option value="PSEUDOCAP">PSEUDOCAP</option> + <option value="PUBMED">PUBMED</option> + <option value="PUBMED_POMBASE">PUBMED_POMBASE</option> + <option value="RAP_GENE">RAP_GENE</option> + <option value="REACTOME">REACTOME</option> + <option value="REBASE">REBASE</option> + <option value="REFSEQ">REFSEQ</option> + <option value="REFSEQ_DNA">REFSEQ_DNA</option> + <option value="REFSEQ_DNA_PREDICTED">REFSEQ_DNA_PREDICTED</option> + <option value="REFSEQ_MRNA">REFSEQ_MRNA</option> + <option value="REFSEQ_MRNA_PREDICTED">REFSEQ_MRNA_PREDICTED</option> + <option value="REFSEQ_NCRNA">REFSEQ_NCRNA</option> + <option value="REFSEQ_NCRNA_PREDICTED">REFSEQ_NCRNA_PREDICTED</option> + <option value="REFSEQ_PEPTIDE">REFSEQ_PEPTIDE</option> + <option value="REFSEQ_PEPTIDE_PREDICTED">REFSEQ_PEPTIDE_PREDICTED</option> + <option value="RFAM">RFAM</option> + <option value="RFAM_GENE">RFAM_GENE</option> + <option value="RFAM_TRANS_NAME">RFAM_TRANS_NAME</option> + <option value="RHEA">RHEA</option> + <option value="RIBOSOMAL_PROTEIN_GENE_DATABASE">RIBOSOMAL_PROTEIN_GENE_DATABASE</option> + <option value="RNAMMER">RNAMMER</option> + <option value="SCHISTODB">SCHISTODB</option> + <option value="SGD">SGD</option> + <option value="SGD_GENE">SGD_GENE</option> + <option value="SGD_TRANSCRIPT">SGD_TRANSCRIPT</option> + <option value="SMAR_COMMUNITY_ANNOTATION">SMAR_COMMUNITY_ANNOTATION</option> + <option value="SO">SO</option> + <option value="SPBASE">SPBASE</option> + <option value="SPD">SPD</option> + <option value="STRING">STRING</option> + <option value="SUBTILIST">SUBTILIST</option> + <option value="SWISS_MODEL">SWISS_MODEL</option> + <option value="TAIR_LOCUS">TAIR_LOCUS</option> + <option value="TAIR_SYMBOL">TAIR_SYMBOL</option> + <option value="TIGR_GENEINDEX">TIGR_GENEINDEX</option> + <option value="TIGR_LOCUS">TIGR_LOCUS</option> + <option value="TRANSFAC">TRANSFAC</option> + <option value="TRIAD_JGI_V1.0">TRIAD_JGI_V1.0</option> + <option value="TRNASCAN_SE">TRNASCAN_SE</option> + <option value="TUBERCULIST">TUBERCULIST</option> + <option value="TUBER_GENOSCOPE_GENE">TUBER_GENOSCOPE_GENE</option> + <option value="UNIGENE">UNIGENE</option> + <option value="UNIPARC">UNIPARC</option> + <option value="UNIPATHWAY">UNIPATHWAY</option> + <option value="UNIPROT">UNIPROT</option> + <option value="VB_COMMUNITY_ANNOTATION">VB_COMMUNITY_ANNOTATION</option> + <option value="VB_COMMUNITY_SYMBOL">VB_COMMUNITY_SYMBOL</option> + <option value="VB_EXTERNAL_DESCRIPTION">VB_EXTERNAL_DESCRIPTION</option> + <option value="VB_RNA_DESCRIPTION">VB_RNA_DESCRIPTION</option> + <option value="WIKIGENE">WIKIGENE</option> + <option value="WORMBASE_GENE">WORMBASE_GENE</option> + <option value="WORMBASE_GSEQNAME">WORMBASE_GSEQNAME</option> + <option value="WORMBASE_LOCUS">WORMBASE_LOCUS</option> + <option value="WORMBASE_TRANSCRIPT">WORMBASE_TRANSCRIPT</option> + <option value="WORMPEP_ID">WORMPEP_ID</option> + <option value="ZNGP">ZNGP</option> + <option value="collection">collection</option> + <option value="database">database</option> + <option value="description">description</option> + <option value="domain">domain</option> + <option value="domain_source">domain_source</option> + <option value="exon">exon</option> + <option value="gene_name">gene_name</option> + <option value="gene_synonym">gene_synonym</option> + <option value="gene_version">gene_version</option> + <option value="genetree">genetree</option> + <option value="genomic_unit">genomic_unit</option> + <option value="haplotype">haplotype</option> + <option value="id">id</option> + <option value="id_noversion">id_noversion</option> + <option value="name">name</option> + <option value="peptide">peptide</option> + <option value="peptide_version">peptide_version</option> + <option value="probe">probe</option> + <option value="probeset">probeset</option> + <option value="seq_region_name">seq_region_name</option> + <option value="source">source</option> + <option value="species">species</option> + <option value="system_name">system_name</option> + <option value="transcript">transcript</option> + <option value="transcript_version">transcript_version</option> + </param> + <conditional name="comp_operation"> + <param name="operation" type="select" label="Comparison operation" > + <option value="equal">equal</option> + <option value="not">not</option> + <option value="range">range</option> + </param> + <when value="equal"> + <param name="query_text" type="text" label="Searched term"/> + </when> + <when value="not"> + <param name="query_text" type="text" label="Searched term"/> + <param name="not_query_text" type="text" label="Limiting term"/> + </when> + <when value="range"> + <param name="min" type="text" label="From"/> + <param name="max" type="text" label="To"/> + </when> + </conditional> + </repeat> + </when> + + <when value="ensemblGenomes_genome"> + <param name="fields" type="select" label="Fields to extract" multiple="true"> + <option value="NCBI_TAXONOMY_ID" selected="true">NCBI_TAXONOMY_ID</option> + <option value="assembly_accession" selected="true">assembly_accession</option> + <option value="assembly_name" selected="true">assembly_name</option> + <option value="creation_date" selected="true">creation_date</option> + <option value="display_name" selected="true">display_name</option> + <option value="domain_source" selected="true">domain_source</option> + <option value="genebuild" selected="true">genebuild</option> + <option value="genomic_unit" selected="true">genomic_unit</option> + <option value="has_genome_alignments" selected="true">has_genome_alignments</option> + <option value="has_other_alignments" selected="true">has_other_alignments</option> + <option value="has_pan_compara" selected="true">has_pan_compara</option> + <option value="has_variations" selected="true">has_variations</option> + <option value="id" selected="true">id</option> + <option value="last_modification_date" selected="true">last_modification_date</option> + <option value="name" selected="true">name</option> + <option value="production_name" selected="true">production_name</option> + <option value="strain" selected="true">strain</option> + <validator type="no_options" message="Please select at least one field" /> + </param> + <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> + <param name="query_field" type="select" label="Fields" > + <option value="NCBI_TAXONOMY_ID">NCBI_TAXONOMY_ID</option> + <option value="alias">alias</option> + <option value="assembly_accession">assembly_accession</option> + <option value="assembly_default">assembly_default</option> + <option value="assembly_name">assembly_name</option> + <option value="classification">classification</option> + <option value="collection">collection</option> + <option value="common_name">common_name</option> + <option value="creation_date">creation_date</option> + <option value="display_name">display_name</option> + <option value="division">division</option> + <option value="domain_source">domain_source</option> + <option value="genebuild">genebuild</option> + <option value="genomic_unit">genomic_unit</option> + <option value="has_genome_alignments">has_genome_alignments</option> + <option value="has_other_alignments">has_other_alignments</option> + <option value="has_pan_compara">has_pan_compara</option> + <option value="has_variations">has_variations</option> + <option value="id">id</option> + <option value="last_modification_date">last_modification_date</option> + <option value="name">name</option> + <option value="production_name">production_name</option> + <option value="scientific_name">scientific_name</option> + <option value="strain">strain</option> + </param> + <conditional name="comp_operation"> + <param name="operation" type="select" label="Comparison operation" > + <option value="equal">equal</option> + <option value="not">not</option> + <option value="range">range</option> + </param> + <when value="equal"> + <param name="query_text" type="text" label="Searched term"/> + </when> + <when value="not"> + <param name="query_text" type="text" label="Searched term"/> + <param name="not_query_text" type="text" label="Limiting term"/> + </when> + <when value="range"> + <param name="min" type="text" label="From"/> + <param name="max" type="text" label="To"/> + </when> + </conditional> + </repeat> + </when> + + <when value="ensemblGenomes_seqRegion"> + <param name="fields" type="select" label="Fields to extract" multiple="true"> + <option value="NCBI_TAXONOMY_ID" selected="true">NCBI_TAXONOMY_ID</option> + <option value="coord_system" selected="true">coord_system</option> + <option value="domain_source" selected="true">domain_source</option> + <option value="genomic_unit" selected="true">genomic_unit</option> + <option value="id" selected="true">id</option> + <option value="length" selected="true">length</option> + <option value="location" selected="true">location</option> + <option value="name" selected="true">name</option> + <option value="production_name" selected="true">production_name</option> + <option value="species" selected="true">species</option> + <validator type="no_options" message="Please select at least one field" /> + </param> + <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> + <param name="query_field" type="select" label="Fields" > + <option value="NCBI_TAXONOMY_ID">NCBI_TAXONOMY_ID</option> + <option value="coord_system">coord_system</option> + <option value="domain_source">domain_source</option> + <option value="genomic_unit">genomic_unit</option> + <option value="id">id</option> + <option value="id_noversion">id_noversion</option> + <option value="name">name</option> + <option value="production_name">production_name</option> + <option value="species">species</option> + </param> + <conditional name="comp_operation"> + <param name="operation" type="select" label="Comparison operation" > + <option value="equal">equal</option> + <option value="not">not</option> + <option value="range">range</option> + </param> + <when value="equal"> + <param name="query_text" type="text" label="Searched term"/> + </when> + <when value="not"> + <param name="query_text" type="text" label="Searched term"/> + <param name="not_query_text" type="text" label="Limiting term"/> + </when> + <when value="range"> + <param name="min" type="text" label="From"/> + <param name="max" type="text" label="To"/> + </when> + </conditional> + </repeat> + </when> + + <when value="ensemblGenomes_variant"> + <param name="fields" type="select" label="Fields to extract" multiple="true"> + <option value="NCBI_TAXONOMY_ID" selected="true">NCBI_TAXONOMY_ID</option> + <option value="associated_gene" selected="true">associated_gene</option> + <option value="description" selected="true">description</option> + <option value="domain_source" selected="true">domain_source</option> + <option value="genomic_unit" selected="true">genomic_unit</option> + <option value="id" selected="true">id</option> + <option value="name" selected="true">name</option> + <option value="phenotype" selected="true">phenotype</option> + <option value="production_name" selected="true">production_name</option> + <option value="species" selected="true">species</option> + <option value="study" selected="true">study</option> + <option value="synonym" selected="true">synonym</option> + <option value="variation_source" selected="true">variation_source</option> + <validator type="no_options" message="Please select at least one field" /> + </param> + <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> + <param name="query_field" type="select" label="Fields" > + <option value="NCBI_TAXONOMY_ID">NCBI_TAXONOMY_ID</option> + <option value="associated_gene">associated_gene</option> + <option value="description">description</option> + <option value="domain_source">domain_source</option> + <option value="genomic_unit">genomic_unit</option> + <option value="id">id</option> + <option value="id_noversion">id_noversion</option> + <option value="name">name</option> + <option value="phenotype">phenotype</option> + <option value="production_name">production_name</option> + <option value="species">species</option> + <option value="study">study</option> + <option value="synonym">synonym</option> + <option value="variation_source">variation_source</option> + </param> + <conditional name="comp_operation"> + <param name="operation" type="select" label="Comparison operation" > + <option value="equal">equal</option> + <option value="not">not</option> + <option value="range">range</option> + </param> + <when value="equal"> + <param name="query_text" type="text" label="Searched term"/> + </when> + <when value="not"> + <param name="query_text" type="text" label="Searched term"/> + <param name="not_query_text" type="text" label="Limiting term"/> + </when> + <when value="range"> + <param name="min" type="text" label="From"/> + <param name="max" type="text" label="To"/> + </when> + </conditional> + </repeat> + </when> + + <when value="enzymeportal"> + <param name="fields" type="select" label="Fields to extract" multiple="true"> + <option value="CHEBI" selected="true">CHEBI</option> + <option value="CHEMBL" selected="true">CHEMBL</option> + <option value="INTENZ" selected="true">INTENZ</option> + <option value="OMIM" selected="true">OMIM</option> + <option value="REACTOME" selected="true">REACTOME</option> + <option value="TAXONOMY" selected="true">TAXONOMY</option> + <option value="UNIPROTKB" selected="true">UNIPROTKB</option> + <option value="acc" selected="true">acc</option> + <option value="common_name" selected="true">common_name</option> + <option value="description" selected="true">description</option> + <option value="domain_source" selected="true">domain_source</option> + <option value="id" selected="true">id</option> + <option value="name" selected="true">name</option> + <option value="scientific_name" selected="true">scientific_name</option> + <option value="status" selected="true">status</option> + <validator type="no_options" message="Please select at least one field" /> + </param> + <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> + <param name="query_field" type="select" label="Fields" > + <option value="CHEBI">CHEBI</option> + <option value="CHEMBL">CHEMBL</option> + <option value="INTENZ">INTENZ</option> + <option value="OMIM">OMIM</option> + <option value="REACTOME">REACTOME</option> + <option value="TAXONOMY">TAXONOMY</option> + <option value="UNIPROTKB">UNIPROTKB</option> + <option value="acc">acc</option> + <option value="common_name">common_name</option> + <option value="compound_name">compound_name</option> + <option value="compound_type">compound_type</option> + <option value="description">description</option> + <option value="disease_name">disease_name</option> + <option value="domain_source">domain_source</option> + <option value="gene_name">gene_name</option> + <option value="id">id</option> + <option value="name">name</option> + <option value="scientific_name">scientific_name</option> + <option value="status">status</option> + <option value="synonym">synonym</option> + </param> + <conditional name="comp_operation"> + <param name="operation" type="select" label="Comparison operation" > + <option value="equal">equal</option> + <option value="not">not</option> + <option value="range">range</option> + </param> + <when value="equal"> + <param name="query_text" type="text" label="Searched term"/> + </when> + <when value="not"> + <param name="query_text" type="text" label="Searched term"/> + <param name="not_query_text" type="text" label="Limiting term"/> + </when> + <when value="range"> + <param name="min" type="text" label="From"/> + <param name="max" type="text" label="To"/> + </when> + </conditional> + </repeat> + </when> + + <when value="enzymeportal_enzymes"> + <param name="fields" type="select" label="Fields to extract" multiple="true"> + <option value="CHEBI" selected="true">CHEBI</option> + <option value="CHEMBL" selected="true">CHEMBL</option> + <option value="INTENZ" selected="true">INTENZ</option> + <option value="OMIM" selected="true">OMIM</option> + <option value="REACTOME" selected="true">REACTOME</option> + <option value="TAXONOMY" selected="true">TAXONOMY</option> + <option value="UNIPROTKB" selected="true">UNIPROTKB</option> + <option value="common_name" selected="true">common_name</option> + <option value="compound_name" selected="true">compound_name</option> + <option value="compound_type" selected="true">compound_type</option> + <option value="description" selected="true">description</option> + <option value="disease_name" selected="true">disease_name</option> + <option value="domain_source" selected="true">domain_source</option> + <option value="enzyme_family" selected="true">enzyme_family</option> + <option value="gene_name" selected="true">gene_name</option> + <option value="id" selected="true">id</option> + <option value="name" selected="true">name</option> + <option value="protein_name" selected="true">protein_name</option> + <option value="scientific_name" selected="true">scientific_name</option> + <option value="synonym" selected="true">synonym</option> + <option value="uniprot_name" selected="true">uniprot_name</option> + <validator type="no_options" message="Please select at least one field" /> + </param> + <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> + <param name="query_field" type="select" label="Fields" > + <option value="CHEBI">CHEBI</option> + <option value="CHEMBL">CHEMBL</option> + <option value="INTENZ">INTENZ</option> + <option value="OMIM">OMIM</option> + <option value="REACTOME">REACTOME</option> + <option value="TAXONOMY">TAXONOMY</option> + <option value="UNIPROTKB">UNIPROTKB</option> + <option value="common_name">common_name</option> + <option value="compound_name">compound_name</option> + <option value="compound_type">compound_type</option> + <option value="description">description</option> + <option value="disease_name">disease_name</option> + <option value="domain_source">domain_source</option> + <option value="enzyme_family">enzyme_family</option> + <option value="gene_name">gene_name</option> + <option value="id">id</option> + <option value="name">name</option> + <option value="protein_name">protein_name</option> + <option value="scientific_name">scientific_name</option> + <option value="synonym">synonym</option> + <option value="uniprot_name">uniprot_name</option> + </param> + <conditional name="comp_operation"> + <param name="operation" type="select" label="Comparison operation" > + <option value="equal">equal</option> + <option value="not">not</option> + <option value="range">range</option> + </param> + <when value="equal"> + <param name="query_text" type="text" label="Searched term"/> + </when> + <when value="not"> + <param name="query_text" type="text" label="Searched term"/> + <param name="not_query_text" type="text" label="Limiting term"/> + </when> + <when value="range"> + <param name="min" type="text" label="From"/> + <param name="max" type="text" label="To"/> + </when> + </conditional> + </repeat> + </when> + + <when value="atlas-experiments"> + <param name="fields" type="select" label="Fields to extract" multiple="true"> + <option value="ARRAYEXPRESS" selected="true">ARRAYEXPRESS</option> + <option value="ENSEMBL" selected="true">ENSEMBL</option> + <option value="PUBMED" selected="true">PUBMED</option> + <option value="TAXONOMY" selected="true">TAXONOMY</option> + <option value="data_protocol" selected="true">data_protocol</option> + <option value="dataset_file" selected="true">dataset_file</option> + <option value="description" selected="true">description</option> + <option value="disease" selected="true">disease</option> + <option value="domain_source" selected="true">domain_source</option> + <option value="full_dataset_link" selected="true">full_dataset_link</option> + <option value="id" selected="true">id</option> + <option value="name" selected="true">name</option> + <option value="omics_type" selected="true">omics_type</option> + <option value="publication_date" selected="true">publication_date</option> + <option value="sample_protocol" selected="true">sample_protocol</option> + <validator type="no_options" message="Please select at least one field" /> + </param> + <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> + <param name="query_field" type="select" label="Fields" > + <option value="ARRAYEXPRESS">ARRAYEXPRESS</option> + <option value="ENSEMBL">ENSEMBL</option> + <option value="PUBMED">PUBMED</option> + <option value="TAXONOMY">TAXONOMY</option> + <option value="acc">acc</option> + <option value="age">age</option> + <option value="biopsy_site">biopsy_site</option> + <option value="biotic_plant_treatment">biotic_plant_treatment</option> + <option value="block">block</option> + <option value="breed">breed</option> + <option value="cell_cycle_stage">cell_cycle_stage</option> + <option value="cell_line">cell_line</option> + <option value="cell_type">cell_type</option> + <option value="cellular_component">cellular_component</option> + <option value="chromosomal_aberration">chromosomal_aberration</option> + <option value="clinical_history">clinical_history</option> + <option value="clinical_information">clinical_information</option> + <option value="clinical_treatment">clinical_treatment</option> + <option value="compound">compound</option> + <option value="creation_date">creation_date</option> + <option value="cultivar">cultivar</option> + <option value="data_protocol">data_protocol</option> + <option value="data_synonyms">data_synonyms</option> + <option value="description">description</option> + <option value="description_synonyms">description_synonyms</option> + <option value="developmental_stage">developmental_stage</option> + <option value="diet">diet</option> + <option value="disease">disease</option> + <option value="disease_staging">disease_staging</option> + <option value="domain_source">domain_source</option> + <option value="ecotype">ecotype</option> + <option value="environmental_history">environmental_history</option> + <option value="environmental_stress">environmental_stress</option> + <option value="estrogen_receptor_status">estrogen_receptor_status</option> + <option value="family_relationship">family_relationship</option> + <option value="fraction">fraction</option> + <option value="full_dataset_link">full_dataset_link</option> + <option value="generation">generation</option> + <option value="genetic_modification">genetic_modification</option> + <option value="genotype">genotype</option> + <option value="gestational_age">gestational_age</option> + <option value="growth_condition">growth_condition</option> + <option value="histology">histology</option> + <option value="id">id</option> + <option value="individual">individual</option> + <option value="infect">infect</option> + <option value="injury">injury</option> + <option value="irradiate">irradiate</option> + <option value="last_modification_date">last_modification_date</option> + <option value="light">light</option> + <option value="material_type">material_type</option> + <option value="name">name</option> + <option value="name_synonyms">name_synonyms</option> + <option value="omics_type">omics_type</option> + <option value="organism_part">organism_part</option> + <option value="passage">passage</option> + <option value="phenotype">phenotype</option> + <option value="physical_activity">physical_activity</option> + <option value="ploidy">ploidy</option> + <option value="population">population</option> + <option value="pregnancy">pregnancy</option> + <option value="protocol">protocol</option> + <option value="publication_date">publication_date</option> + <option value="repository">repository</option> + <option value="rna">rna</option> + <option value="rna_interference">rna_interference</option> + <option value="sample_protocol">sample_protocol</option> + <option value="sample_synonyms">sample_synonyms</option> + <option value="sampling_site">sampling_site</option> + <option value="sampling_time">sampling_time</option> + <option value="sampling_time_point">sampling_time_point</option> + <option value="sex">sex</option> + <option value="software">software</option> + <option value="specimen_with_known_storage_state">specimen_with_known_storage_state</option> + <option value="stimulus">stimulus</option> + <option value="strain">strain</option> + <option value="survival_time">survival_time</option> + <option value="temperature">temperature</option> + <option value="time">time</option> + <option value="treatment">treatment</option> + <option value="tumor_grading">tumor_grading</option> + <option value="tumor_stage">tumor_stage</option> + </param> + <conditional name="comp_operation"> + <param name="operation" type="select" label="Comparison operation" > + <option value="equal">equal</option> + <option value="not">not</option> + <option value="range">range</option> + </param> + <when value="equal"> + <param name="query_text" type="text" label="Searched term"/> + </when> + <when value="not"> + <param name="query_text" type="text" label="Searched term"/> + <param name="not_query_text" type="text" label="Limiting term"/> + </when> + <when value="range"> + <param name="min" type="text" label="From"/> + <param name="max" type="text" label="To"/> + </when> + </conditional> + </repeat> + </when> + + <when value="gnps"> + <param name="fields" type="select" label="Fields to extract" multiple="true"> + <option value="PUBMED" selected="true">PUBMED</option> + <option value="TAXONOMY" selected="true">TAXONOMY</option> + <option value="dataset_file" selected="true">dataset_file</option> + <option value="description" selected="true">description</option> + <option value="domain_source" selected="true">domain_source</option> + <option value="full_dataset_link" selected="true">full_dataset_link</option> + <option value="id" selected="true">id</option> + <option value="instrument_platform" selected="true">instrument_platform</option> + <option value="modification" selected="true">modification</option> + <option value="name" selected="true">name</option> + <option value="omics_type" selected="true">omics_type</option> + <option value="species" selected="true">species</option> + <option value="submission_date" selected="true">submission_date</option> + <option value="technology_type" selected="true">technology_type</option> + <validator type="no_options" message="Please select at least one field" /> + </param> + <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> + <param name="query_field" type="select" label="Fields" > + <option value="PUBMED">PUBMED</option> + <option value="TAXONOMY">TAXONOMY</option> + <option value="acc">acc</option> + <option value="curator_keywords">curator_keywords</option> + <option value="description">description</option> + <option value="description_synonyms">description_synonyms</option> + <option value="domain_source">domain_source</option> + <option value="full_dataset_link">full_dataset_link</option> + <option value="id">id</option> + <option value="instrument_platform">instrument_platform</option> + <option value="modification">modification</option> + <option value="name">name</option> + <option value="name_synonyms">name_synonyms</option> + <option value="omics_type">omics_type</option> + <option value="pubmed_abstract">pubmed_abstract</option> + <option value="pubmed_abstract_synonyms">pubmed_abstract_synonyms</option> + <option value="pubmed_authors">pubmed_authors</option> + <option value="pubmed_title">pubmed_title</option> + <option value="pubmed_title_synonyms">pubmed_title_synonyms</option> + <option value="repository">repository</option> + <option value="species">species</option> + <option value="submission_date">submission_date</option> + <option value="submitter">submitter</option> + <option value="technology_type">technology_type</option> + </param> + <conditional name="comp_operation"> + <param name="operation" type="select" label="Comparison operation" > + <option value="equal">equal</option> + <option value="not">not</option> + <option value="range">range</option> + </param> + <when value="equal"> + <param name="query_text" type="text" label="Searched term"/> + </when> + <when value="not"> + <param name="query_text" type="text" label="Searched term"/> + <param name="not_query_text" type="text" label="Limiting term"/> + </when> + <when value="range"> + <param name="min" type="text" label="From"/> + <param name="max" type="text" label="To"/> + </when> + </conditional> + </repeat> + </when> + + <when value="go"> + <param name="fields" type="select" label="Fields to extract" multiple="true"> + <option value="ARACYC" selected="true">ARACYC</option> + <option value="BIOCYC" selected="true">BIOCYC</option> + <option value="BRENDA" selected="true">BRENDA</option> + <option value="CHEBI" selected="true">CHEBI</option> + <option value="CORUM" selected="true">CORUM</option> + <option value="DICTYBASE_REF" selected="true">DICTYBASE_REF</option> + <option value="DOI" selected="true">DOI</option> + <option value="EC" selected="true">EC</option> + <option value="EMBL" selected="true">EMBL</option> + <option value="FB" selected="true">FB</option> + <option value="FMA" selected="true">FMA</option> + <option value="GO" selected="true">GO</option> + <option value="GOA" selected="true">GOA</option> + <option value="GO_REF" selected="true">GO_REF</option> + <option value="HTTP" selected="true">HTTP</option> + <option value="HTTPS" selected="true">HTTPS</option> + <option value="INTACT" selected="true">INTACT</option> + <option value="INTERPRO" selected="true">INTERPRO</option> + <option value="ISBN" selected="true">ISBN</option> + <option value="IUPHAR_GPCR" selected="true">IUPHAR_GPCR</option> + <option value="IUPHAR_RECEPTOR" selected="true">IUPHAR_RECEPTOR</option> + <option value="JSTOR" selected="true">JSTOR</option> + <option value="KEGG_PATHWAY" selected="true">KEGG_PATHWAY</option> + <option value="LIGAND" selected="true">LIGAND</option> + <option value="MA" selected="true">MA</option> + <option value="MEDLINE" selected="true">MEDLINE</option> + <option value="MEROPS" selected="true">MEROPS</option> + <option value="MEROPS_FAM" selected="true">MEROPS_FAM</option> + <option value="MESH" selected="true">MESH</option> + <option value="METACYC" selected="true">METACYC</option> + <option value="NIF_SUBCELLULAR" selected="true">NIF_SUBCELLULAR</option> + <option value="OMIM" selected="true">OMIM</option> + <option value="PDB" selected="true">PDB</option> + <option value="PFAM" selected="true">PFAM</option> + <option value="PMID" selected="true">PMID</option> + <option value="PO" selected="true">PO</option> + <option value="PR" selected="true">PR</option> + <option value="PROSITE" selected="true">PROSITE</option> + <option value="PSI-MOD" selected="true">PSI-MOD</option> + <option value="PUBCHEM" selected="true">PUBCHEM</option> + <option value="PUBCHEM_COMPOUND" selected="true">PUBCHEM_COMPOUND</option> + <option value="PUBMED" selected="true">PUBMED</option> + <option value="REACTOME" selected="true">REACTOME</option> + <option value="RESID" selected="true">RESID</option> + <option value="RHEA" selected="true">RHEA</option> + <option value="RNAMODS" selected="true">RNAMODS</option> + <option value="SABIO-RK" selected="true">SABIO-RK</option> + <option value="SO" selected="true">SO</option> + <option value="TC" selected="true">TC</option> + <option value="TIGR_TIGRFAMS" selected="true">TIGR_TIGRFAMS</option> + <option value="UBERON" selected="true">UBERON</option> + <option value="UM-BBD_ENZYMEID" selected="true">UM-BBD_ENZYMEID</option> + <option value="UM-BBD_PATHWAYID" selected="true">UM-BBD_PATHWAYID</option> + <option value="UM-BBD_REACTIONID" selected="true">UM-BBD_REACTIONID</option> + <option value="UM-BBD_RULEID" selected="true">UM-BBD_RULEID</option> + <option value="UNIPATHWAY" selected="true">UNIPATHWAY</option> + <option value="UNIPROT" selected="true">UNIPROT</option> + <option value="UNIPROTKB" selected="true">UNIPROTKB</option> + <option value="WBBT" selected="true">WBBT</option> + <option value="WB_REF" selected="true">WB_REF</option> + <option value="WIKI" selected="true">WIKI</option> + <option value="WIKIPEDIA" selected="true">WIKIPEDIA</option> + <option value="ZFIN" selected="true">ZFIN</option> + <option value="alt_id" selected="true">alt_id</option> + <option value="comment" selected="true">comment</option> + <option value="consider" selected="true">consider</option> + <option value="description" selected="true">description</option> + <option value="domain_source" selected="true">domain_source</option> + <option value="id" selected="true">id</option> + <option value="is_a" selected="true">is_a</option> + <option value="is_obsolete" selected="true">is_obsolete</option> + <option value="is_root" selected="true">is_root</option> + <option value="name" selected="true">name</option> + <option value="namespace" selected="true">namespace</option> + <option value="negatively_regulates" selected="true">negatively_regulates</option> + <option value="part_of" selected="true">part_of</option> + <option value="positively_regulates" selected="true">positively_regulates</option> + <option value="regulates" selected="true">regulates</option> + <option value="replaced_by" selected="true">replaced_by</option> + <option value="subset" selected="true">subset</option> + <option value="synonym" selected="true">synonym</option> + <validator type="no_options" message="Please select at least one field" /> + </param> + <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> + <param name="query_field" type="select" label="Fields" > + <option value="ARACYC">ARACYC</option> + <option value="BIOCYC">BIOCYC</option> + <option value="BRENDA">BRENDA</option> + <option value="CHEBI">CHEBI</option> + <option value="CL">CL</option> + <option value="CORUM">CORUM</option> + <option value="DDANAT">DDANAT</option> + <option value="DICTYBASE_REF">DICTYBASE_REF</option> + <option value="DOI">DOI</option> + <option value="EC">EC</option> + <option value="EMBL">EMBL</option> + <option value="FB">FB</option> + <option value="FBBT">FBBT</option> + <option value="FMA">FMA</option> + <option value="GO">GO</option> + <option value="GOA">GOA</option> + <option value="GOC">GOC</option> + <option value="GOCL">GOCL</option> + <option value="GOV">GOV</option> + <option value="GO_REF">GO_REF</option> + <option value="GPC">GPC</option> + <option value="HTTP">HTTP</option> + <option value="HTTPS">HTTPS</option> + <option value="IMG">IMG</option> + <option value="INTACT">INTACT</option> + <option value="INTERPRO">INTERPRO</option> + <option value="ISBN">ISBN</option> + <option value="ISSN">ISSN</option> + <option value="IUPHAR_GPCR">IUPHAR_GPCR</option> + <option value="IUPHAR_RECEPTOR">IUPHAR_RECEPTOR</option> + <option value="JSTOR">JSTOR</option> + <option value="KEGG">KEGG</option> + <option value="KEGG_PATHWAY">KEGG_PATHWAY</option> + <option value="LIGAND">LIGAND</option> + <option value="MA">MA</option> + <option value="MEDLINE">MEDLINE</option> + <option value="MEROPS">MEROPS</option> + <option value="MEROPS_FAM">MEROPS_FAM</option> + <option value="MESH">MESH</option> + <option value="METACYC">METACYC</option> + <option value="MITRE">MITRE</option> + <option value="MP">MP</option> + <option value="MSH">MSH</option> + <option value="NIF_SUBCELLULAR">NIF_SUBCELLULAR</option> + <option value="OMIM">OMIM</option> + <option value="PATO">PATO</option> + <option value="PDB">PDB</option> + <option value="PFAM">PFAM</option> + <option value="PHI">PHI</option> + <option value="PMID">PMID</option> + <option value="PMIG">PMIG</option> + <option value="PO">PO</option> + <option value="POC">POC</option> + <option value="PO_REF">PO_REF</option> + <option value="PR">PR</option> + <option value="PROSITE">PROSITE</option> + <option value="PSI-MOD">PSI-MOD</option> + <option value="PUBCHEM">PUBCHEM</option> + <option value="PUBCHEM_COMPOUND">PUBCHEM_COMPOUND</option> + <option value="PUBMED">PUBMED</option> + <option value="REACTOME">REACTOME</option> + <option value="RESID">RESID</option> + <option value="RHEA">RHEA</option> + <option value="RNAMODS">RNAMODS</option> + <option value="SABIO-RK">SABIO-RK</option> + <option value="SO">SO</option> + <option value="SP">SP</option> + <option value="TC">TC</option> + <option value="TIGR_TIGRFAMS">TIGR_TIGRFAMS</option> + <option value="UBERON">UBERON</option> + <option value="UM-BBD_ENZYMEID">UM-BBD_ENZYMEID</option> + <option value="UM-BBD_PATHWAYID">UM-BBD_PATHWAYID</option> + <option value="UM-BBD_REACTIONID">UM-BBD_REACTIONID</option> + <option value="UM-BBD_RULEID">UM-BBD_RULEID</option> + <option value="UNIPATHWAY">UNIPATHWAY</option> + <option value="UNIPROT">UNIPROT</option> + <option value="UNIPROTKB">UNIPROTKB</option> + <option value="UNIPROTKB-KW">UNIPROTKB-KW</option> + <option value="URL">URL</option> + <option value="VZ">VZ</option> + <option value="WBBT">WBBT</option> + <option value="WB_REF">WB_REF</option> + <option value="WIKI">WIKI</option> + <option value="WIKIPEDIA">WIKIPEDIA</option> + <option value="XAO">XAO</option> + <option value="ZFA">ZFA</option> + <option value="ZFIN">ZFIN</option> + <option value="alt_id">alt_id</option> + <option value="comment">comment</option> + <option value="consider">consider</option> + <option value="description">description</option> + <option value="domain_source">domain_source</option> + <option value="id">id</option> + <option value="is_a">is_a</option> + <option value="is_obsolete">is_obsolete</option> + <option value="is_root">is_root</option> + <option value="name">name</option> + <option value="namespace">namespace</option> + <option value="negatively_regulates">negatively_regulates</option> + <option value="part_of">part_of</option> + <option value="positively_regulates">positively_regulates</option> + <option value="regulates">regulates</option> + <option value="replaced_by">replaced_by</option> + <option value="subset">subset</option> + <option value="synonym">synonym</option> + </param> + <conditional name="comp_operation"> + <param name="operation" type="select" label="Comparison operation" > + <option value="equal">equal</option> + <option value="not">not</option> + <option value="range">range</option> + </param> + <when value="equal"> + <param name="query_text" type="text" label="Searched term"/> + </when> + <when value="not"> + <param name="query_text" type="text" label="Searched term"/> + <param name="not_query_text" type="text" label="Limiting term"/> + </when> + <when value="range"> + <param name="min" type="text" label="From"/> + <param name="max" type="text" label="To"/> + </when> + </conditional> + </repeat> + </when> + + <when value="gpcrdb"> + <param name="fields" type="select" label="Fields to extract" multiple="true"> + <option value="SWISSPROT" selected="true">SWISSPROT</option> + <option value="TAXONOMY" selected="true">TAXONOMY</option> + <option value="TREMBL" selected="true">TREMBL</option> + <option value="description" selected="true">description</option> + <option value="domain_source" selected="true">domain_source</option> + <option value="gpcr-family" selected="true">gpcr-family</option> + <option value="id" selected="true">id</option> + <option value="name" selected="true">name</option> + <validator type="no_options" message="Please select at least one field" /> + </param> + <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> + <param name="query_field" type="select" label="Fields" > + <option value="SWISSPROT">SWISSPROT</option> + <option value="TAXONOMY">TAXONOMY</option> + <option value="TREMBL">TREMBL</option> + <option value="description">description</option> + <option value="domain_source">domain_source</option> + <option value="gpcr-family">gpcr-family</option> + <option value="id">id</option> + <option value="name">name</option> + </param> + <conditional name="comp_operation"> + <param name="operation" type="select" label="Comparison operation" > + <option value="equal">equal</option> + <option value="not">not</option> + <option value="range">range</option> + </param> + <when value="equal"> + <param name="query_text" type="text" label="Searched term"/> + </when> + <when value="not"> + <param name="query_text" type="text" label="Searched term"/> + <param name="not_query_text" type="text" label="Limiting term"/> + </when> + <when value="range"> + <param name="min" type="text" label="From"/> + <param name="max" type="text" label="To"/> + </when> + </conditional> + </repeat> + </when> + + <when value="gpmdb"> + <param name="fields" type="select" label="Fields to extract" multiple="true"> + <option value="ENSEMBL" selected="true">ENSEMBL</option> + <option value="MASSIVE" selected="true">MASSIVE</option> + <option value="PRIDE" selected="true">PRIDE</option> + <option value="PUBMED" selected="true">PUBMED</option> + <option value="description" selected="true">description</option> + <option value="disease" selected="true">disease</option> + <option value="domain_source" selected="true">domain_source</option> + <option value="id" selected="true">id</option> + <option value="instrument_platform" selected="true">instrument_platform</option> + <option value="name" selected="true">name</option> + <option value="omics_type" selected="true">omics_type</option> + <option value="publication" selected="true">publication</option> + <option value="species" selected="true">species</option> + <option value="submission_date" selected="true">submission_date</option> + <validator type="no_options" message="Please select at least one field" /> + </param> + <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> + <param name="query_field" type="select" label="Fields" > + <option value="ENSEMBL">ENSEMBL</option> + <option value="MASSIVE">MASSIVE</option> + <option value="PRIDE">PRIDE</option> + <option value="PUBMED">PUBMED</option> + <option value="brenda_tissue">brenda_tissue</option> + <option value="cell_type">cell_type</option> + <option value="description">description</option> + <option value="description_synonyms">description_synonyms</option> + <option value="disease">disease</option> + <option value="domain_source">domain_source</option> + <option value="id">id</option> + <option value="instrument_platform">instrument_platform</option> + <option value="model">model</option> + <option value="name">name</option> + <option value="name_synonyms">name_synonyms</option> + <option value="omics_type">omics_type</option> + <option value="publication">publication</option> + <option value="pubmed_abstract">pubmed_abstract</option> + <option value="pubmed_authors">pubmed_authors</option> + <option value="pubmed_title">pubmed_title</option> + <option value="repository">repository</option> + <option value="species">species</option> + <option value="submission_date">submission_date</option> + <option value="submitter">submitter</option> + <option value="submitter_affiliation">submitter_affiliation</option> + <option value="submitter_mail">submitter_mail</option> + </param> + <conditional name="comp_operation"> + <param name="operation" type="select" label="Comparison operation" > + <option value="equal">equal</option> + <option value="not">not</option> + <option value="range">range</option> + </param> + <when value="equal"> + <param name="query_text" type="text" label="Searched term"/> + </when> + <when value="not"> + <param name="query_text" type="text" label="Searched term"/> + <param name="not_query_text" type="text" label="Limiting term"/> + </when> + <when value="range"> + <param name="min" type="text" label="From"/> + <param name="max" type="text" label="To"/> + </when> + </conditional> + </repeat> + </when> + + <when value="hgnc"> + <param name="fields" type="select" label="Fields to extract" multiple="true"> + <option value="CCDS" selected="true">CCDS</option> + <option value="EMBL" selected="true">EMBL</option> + <option value="ENSEMBL_GENE" selected="true">ENSEMBL_GENE</option> + <option value="INTENZ" selected="true">INTENZ</option> + <option value="MEDLINE" selected="true">MEDLINE</option> + <option value="MGI" selected="true">MGI</option> + <option value="NCBI" selected="true">NCBI</option> + <option value="OMIM" selected="true">OMIM</option> + <option value="REFSEQ" selected="true">REFSEQ</option> + <option value="RGD" selected="true">RGD</option> + <option value="TAXONOMY" selected="true">TAXONOMY</option> + <option value="UCSC" selected="true">UCSC</option> + <option value="UNIPROT" selected="true">UNIPROT</option> + <option value="VEGA" selected="true">VEGA</option> + <option value="domain_source" selected="true">domain_source</option> + <option value="gd_aliases" selected="true">gd_aliases</option> + <option value="gd_app_name" selected="true">gd_app_name</option> + <option value="gd_app_sym" selected="true">gd_app_sym</option> + <option value="gd_gene_fam_name" selected="true">gd_gene_fam_name</option> + <option value="gd_locus_type" selected="true">gd_locus_type</option> + <option value="gd_prev_sym" selected="true">gd_prev_sym</option> + <option value="gd_pub_chrom_map" selected="true">gd_pub_chrom_map</option> + <option value="gd_status" selected="true">gd_status</option> + <option value="id" selected="true">id</option> + <option value="id_without_prefix" selected="true">id_without_prefix</option> + <validator type="no_options" message="Please select at least one field" /> + </param> + <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> + <param name="query_field" type="select" label="Fields" > + <option value="CCDS">CCDS</option> + <option value="EMBL">EMBL</option> + <option value="ENSEMBL_GENE">ENSEMBL_GENE</option> + <option value="INTENZ">INTENZ</option> + <option value="MEDLINE">MEDLINE</option> + <option value="MGI">MGI</option> + <option value="NCBI">NCBI</option> + <option value="OMIM">OMIM</option> + <option value="REFSEQ">REFSEQ</option> + <option value="RGD">RGD</option> + <option value="TAXONOMY">TAXONOMY</option> + <option value="UCSC">UCSC</option> + <option value="UNIPROT">UNIPROT</option> + <option value="VEGA">VEGA</option> + <option value="domain_source">domain_source</option> + <option value="gd_aliases">gd_aliases</option> + <option value="gd_app_name">gd_app_name</option> + <option value="gd_app_sym">gd_app_sym</option> + <option value="gd_gene_fam_name">gd_gene_fam_name</option> + <option value="gd_locus_type">gd_locus_type</option> + <option value="gd_prev_sym">gd_prev_sym</option> + <option value="gd_pub_chrom_map">gd_pub_chrom_map</option> + <option value="gd_status">gd_status</option> + <option value="id">id</option> + <option value="id_without_prefix">id_without_prefix</option> + </param> + <conditional name="comp_operation"> + <param name="operation" type="select" label="Comparison operation" > + <option value="equal">equal</option> + <option value="not">not</option> + <option value="range">range</option> + </param> + <when value="equal"> + <param name="query_text" type="text" label="Searched term"/> + </when> + <when value="not"> + <param name="query_text" type="text" label="Searched term"/> + <param name="not_query_text" type="text" label="Limiting term"/> + </when> + <when value="range"> + <param name="min" type="text" label="From"/> + <param name="max" type="text" label="To"/> + </when> + </conditional> + </repeat> + </when> + + <when value="human_diseases"> + <param name="fields" type="select" label="Fields to extract" multiple="true"> + <option value="KW" selected="true">KW</option> + <option value="MEDGEN" selected="true">MEDGEN</option> + <option value="MESH" selected="true">MESH</option> + <option value="MIM" selected="true">MIM</option> + <option value="description" selected="true">description</option> + <option value="domain_source" selected="true">domain_source</option> + <option value="id" selected="true">id</option> + <option value="name" selected="true">name</option> + <validator type="no_options" message="Please select at least one field" /> + </param> + <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> + <param name="query_field" type="select" label="Fields" > + <option value="KW">KW</option> + <option value="MEDGEN">MEDGEN</option> + <option value="MESH">MESH</option> + <option value="MIM">MIM</option> + <option value="acronym">acronym</option> + <option value="description">description</option> + <option value="domain_source">domain_source</option> + <option value="id">id</option> + <option value="keyword">keyword</option> + <option value="name">name</option> + <option value="synonym">synonym</option> + </param> + <conditional name="comp_operation"> + <param name="operation" type="select" label="Comparison operation" > + <option value="equal">equal</option> + <option value="not">not</option> + <option value="range">range</option> + </param> + <when value="equal"> + <param name="query_text" type="text" label="Searched term"/> + </when> + <when value="not"> + <param name="query_text" type="text" label="Searched term"/> + <param name="not_query_text" type="text" label="Limiting term"/> + </when> + <when value="range"> + <param name="min" type="text" label="From"/> + <param name="max" type="text" label="To"/> + </when> + </conditional> + </repeat> + </when> + + <when value="imgt-hla"> + <param name="fields" type="select" label="Fields to extract" multiple="true"> + <option value="EMBL-ENA" selected="true">EMBL-ENA</option> + <option value="PUBMED" selected="true">PUBMED</option> + <option value="description" selected="true">description</option> + <option value="domain_source" selected="true">domain_source</option> + <option value="id" selected="true">id</option> + <option value="name" selected="true">name</option> + <option value="organism" selected="true">organism</option> + <validator type="no_options" message="Please select at least one field" /> + </param> + <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> + <param name="query_field" type="select" label="Fields" > + <option value="EMBL-ENA">EMBL-ENA</option> + <option value="PUBMED">PUBMED</option> + <option value="creation_date">creation_date</option> + <option value="description">description</option> + <option value="domain_source">domain_source</option> + <option value="id">id</option> + <option value="last_modification_date">last_modification_date</option> + <option value="name">name</option> + <option value="organism">organism</option> + </param> + <conditional name="comp_operation"> + <param name="operation" type="select" label="Comparison operation" > + <option value="equal">equal</option> + <option value="not">not</option> + <option value="range">range</option> + </param> + <when value="equal"> + <param name="query_text" type="text" label="Searched term"/> + </when> + <when value="not"> + <param name="query_text" type="text" label="Searched term"/> + <param name="not_query_text" type="text" label="Limiting term"/> + </when> + <when value="range"> + <param name="min" type="text" label="From"/> + <param name="max" type="text" label="To"/> + </when> + </conditional> + </repeat> + </when> + + <when value="ipd-kir"> + <param name="fields" type="select" label="Fields to extract" multiple="true"> + <option value="EMBL-ENA" selected="true">EMBL-ENA</option> + <option value="PUBMED" selected="true">PUBMED</option> + <option value="description" selected="true">description</option> + <option value="domain_source" selected="true">domain_source</option> + <option value="id" selected="true">id</option> + <option value="name" selected="true">name</option> + <option value="organism" selected="true">organism</option> + <validator type="no_options" message="Please select at least one field" /> + </param> + <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> + <param name="query_field" type="select" label="Fields" > + <option value="EMBL-ENA">EMBL-ENA</option> + <option value="PUBMED">PUBMED</option> + <option value="creation_date">creation_date</option> + <option value="description">description</option> + <option value="domain_source">domain_source</option> + <option value="id">id</option> + <option value="last_modification_date">last_modification_date</option> + <option value="name">name</option> + <option value="organism">organism</option> + </param> + <conditional name="comp_operation"> + <param name="operation" type="select" label="Comparison operation" > + <option value="equal">equal</option> + <option value="not">not</option> + <option value="range">range</option> + </param> + <when value="equal"> + <param name="query_text" type="text" label="Searched term"/> + </when> + <when value="not"> + <param name="query_text" type="text" label="Searched term"/> + <param name="not_query_text" type="text" label="Limiting term"/> + </when> + <when value="range"> + <param name="min" type="text" label="From"/> + <param name="max" type="text" label="To"/> + </when> + </conditional> + </repeat> + </when> + + <when value="ipd-mhc"> + <param name="fields" type="select" label="Fields to extract" multiple="true"> + <option value="EMBL-ENA" selected="true">EMBL-ENA</option> + <option value="PUBMED" selected="true">PUBMED</option> + <option value="TAXONOMY" selected="true">TAXONOMY</option> + <option value="description" selected="true">description</option> + <option value="domain_source" selected="true">domain_source</option> + <option value="id" selected="true">id</option> + <option value="name" selected="true">name</option> + <option value="organism" selected="true">organism</option> + <validator type="no_options" message="Please select at least one field" /> + </param> + <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> + <param name="query_field" type="select" label="Fields" > + <option value="EMBL-ENA">EMBL-ENA</option> + <option value="PUBMED">PUBMED</option> + <option value="TAXONOMY">TAXONOMY</option> + <option value="creation_date">creation_date</option> + <option value="description">description</option> + <option value="domain_source">domain_source</option> + <option value="id">id</option> + <option value="name">name</option> + <option value="organism">organism</option> + </param> + <conditional name="comp_operation"> + <param name="operation" type="select" label="Comparison operation" > + <option value="equal">equal</option> + <option value="not">not</option> + <option value="range">range</option> + </param> + <when value="equal"> + <param name="query_text" type="text" label="Searched term"/> + </when> + <when value="not"> + <param name="query_text" type="text" label="Searched term"/> + <param name="not_query_text" type="text" label="Limiting term"/> + </when> + <when value="range"> + <param name="min" type="text" label="From"/> + <param name="max" type="text" label="To"/> + </when> + </conditional> + </repeat> + </when> + + <when value="intact-complexes"> + <param name="fields" type="select" label="Fields to extract" multiple="true"> + <option value="CHEMBL" selected="true">CHEMBL</option> + <option value="CHEMBL_TARGET" selected="true">CHEMBL_TARGET</option> + <option value="DIP" selected="true">DIP</option> + <option value="EFO" selected="true">EFO</option> + <option value="EMDB" selected="true">EMDB</option> + <option value="EVIDENCE_ONTOLOGY" selected="true">EVIDENCE_ONTOLOGY</option> + <option value="GO" selected="true">GO</option> + <option value="IMEX" selected="true">IMEX</option> + <option value="INTACT" selected="true">INTACT</option> + <option value="INTACT.INTERACTOR" selected="true">INTACT.INTERACTOR</option> + <option value="INTENZ" selected="true">INTENZ</option> + <option value="INTERPRO" selected="true">INTERPRO</option> + <option value="MATRIXDB" selected="true">MATRIXDB</option> + <option value="MINT" selected="true">MINT</option> + <option value="OMIM" selected="true">OMIM</option> + <option value="ORPHANET" selected="true">ORPHANET</option> + <option value="PDBE" selected="true">PDBE</option> + <option value="PROTEIN_ONTOLOGY" selected="true">PROTEIN_ONTOLOGY</option> + <option value="PUBMED" selected="true">PUBMED</option> + <option value="REACTOME" selected="true">REACTOME</option> + <option value="SIGNOR" selected="true">SIGNOR</option> + <option value="WWPDB" selected="true">WWPDB</option> + <option value="description" selected="true">description</option> + <option value="domain_source" selected="true">domain_source</option> + <option value="id" selected="true">id</option> + <option value="name" selected="true">name</option> + <validator type="no_options" message="Please select at least one field" /> + </param> + <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> + <param name="query_field" type="select" label="Fields" > + <option value="3d-r-factors">3d-r-factors</option> + <option value="CHEMBL">CHEMBL</option> + <option value="CHEMBL_TARGET">CHEMBL_TARGET</option> + <option value="DIP">DIP</option> + <option value="EFO">EFO</option> + <option value="EMDB">EMDB</option> + <option value="EVIDENCE_ONTOLOGY">EVIDENCE_ONTOLOGY</option> + <option value="GO">GO</option> + <option value="IMEX">IMEX</option> + <option value="INTACT">INTACT</option> + <option value="INTACT.INTERACTOR">INTACT.INTERACTOR</option> + <option value="INTENZ">INTENZ</option> + <option value="INTERPRO">INTERPRO</option> + <option value="MATRIXDB">MATRIXDB</option> + <option value="MINT">MINT</option> + <option value="OMIM">OMIM</option> + <option value="ORPHANET">ORPHANET</option> + <option value="PDBE">PDBE</option> + <option value="PROTEIN_ONTOLOGY">PROTEIN_ONTOLOGY</option> + <option value="PUBMED">PUBMED</option> + <option value="REACTOME">REACTOME</option> + <option value="SIGNOR">SIGNOR</option> + <option value="WWPDB">WWPDB</option> + <option value="accepted">accepted</option> + <option value="agonist">agonist</option> + <option value="antagonist">antagonist</option> + <option value="assembly">assembly</option> + <option value="caution">caution</option> + <option value="comment">comment</option> + <option value="commercial_name">commercial_name</option> + <option value="complex-assembly">complex-assembly</option> + <option value="complex-properties">complex-properties</option> + <option value="complex-synonym">complex-synonym</option> + <option value="complex_recommended_name">complex_recommended_name</option> + <option value="complex_synonym">complex_synonym</option> + <option value="complex_systematic_name">complex_systematic_name</option> + <option value="creation_date">creation_date</option> + <option value="curated-complex">curated-complex</option> + <option value="curation_request">curation_request</option> + <option value="description">description</option> + <option value="disease">disease</option> + <option value="domain_source">domain_source</option> + <option value="full_coverage">full_coverage</option> + <option value="gene_name_synonym">gene_name_synonym</option> + <option value="id">id</option> + <option value="interaction_type">interaction_type</option> + <option value="last_modification_date">last_modification_date</option> + <option value="ligand">ligand</option> + <option value="name">name</option> + <option value="remark-internal">remark-internal</option> + <option value="source-text">source-text</option> + <option value="synonym">synonym</option> + </param> + <conditional name="comp_operation"> + <param name="operation" type="select" label="Comparison operation" > + <option value="equal">equal</option> + <option value="not">not</option> + <option value="range">range</option> + </param> + <when value="equal"> + <param name="query_text" type="text" label="Searched term"/> + </when> + <when value="not"> + <param name="query_text" type="text" label="Searched term"/> + <param name="not_query_text" type="text" label="Limiting term"/> + </when> + <when value="range"> + <param name="min" type="text" label="From"/> + <param name="max" type="text" label="To"/> + </when> + </conditional> + </repeat> + </when> + + <when value="intact-experiments"> + <param name="fields" type="select" label="Fields to extract" multiple="true"> + <option value="BRENDA" selected="true">BRENDA</option> + <option value="DOI" selected="true">DOI</option> + <option value="EFO" selected="true">EFO</option> + <option value="EMDB" selected="true">EMDB</option> + <option value="GO" selected="true">GO</option> + <option value="IMEX" selected="true">IMEX</option> + <option value="INTACT" selected="true">INTACT</option> + <option value="INTACT.INTERACTION" selected="true">INTACT.INTERACTION</option> + <option value="MINT" selected="true">MINT</option> + <option value="OMIM" selected="true">OMIM</option> + <option value="PDBE" selected="true">PDBE</option> + <option value="PMC" selected="true">PMC</option> + <option value="PRIDE" selected="true">PRIDE</option> + <option value="PROSITE" selected="true">PROSITE</option> + <option value="PROTEOMEXCHANGE" selected="true">PROTEOMEXCHANGE</option> + <option value="PSI-MI" selected="true">PSI-MI</option> + <option value="PUBMED" selected="true">PUBMED</option> + <option value="RCSB_PDB" selected="true">RCSB_PDB</option> + <option value="UNIPROT_TAXONOMY" selected="true">UNIPROT_TAXONOMY</option> + <option value="WWPDB" selected="true">WWPDB</option> + <option value="description" selected="true">description</option> + <option value="domain_source" selected="true">domain_source</option> + <option value="id" selected="true">id</option> + <option value="name" selected="true">name</option> + <validator type="no_options" message="Please select at least one field" /> + </param> + <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> + <param name="query_field" type="select" label="Fields" > + <option value="BRENDA">BRENDA</option> + <option value="DOI">DOI</option> + <option value="EFO">EFO</option> + <option value="EMDB">EMDB</option> + <option value="GO">GO</option> + <option value="IMEX">IMEX</option> + <option value="IMEX_SOURCE">IMEX_SOURCE</option> + <option value="INTACT">INTACT</option> + <option value="INTACT.INTERACTION">INTACT.INTERACTION</option> + <option value="MINT">MINT</option> + <option value="OMIM">OMIM</option> + <option value="PDBE">PDBE</option> + <option value="PMC">PMC</option> + <option value="PRIDE">PRIDE</option> + <option value="PROSITE">PROSITE</option> + <option value="PROTEOMEXCHANGE">PROTEOMEXCHANGE</option> + <option value="PSI-MI">PSI-MI</option> + <option value="PUBMED">PUBMED</option> + <option value="RCSB_PDB">RCSB_PDB</option> + <option value="UNIPROT_TAXONOMY">UNIPROT_TAXONOMY</option> + <option value="WWPDB">WWPDB</option> + <option value="creation_date">creation_date</option> + <option value="description">description</option> + <option value="domain_source">domain_source</option> + <option value="id">id</option> + <option value="interaction_detection_method">interaction_detection_method</option> + <option value="interaction_type">interaction_type</option> + <option value="last_modification_date">last_modification_date</option> + <option value="name">name</option> + <option value="participant_detection_method">participant_detection_method</option> + </param> + <conditional name="comp_operation"> + <param name="operation" type="select" label="Comparison operation" > + <option value="equal">equal</option> + <option value="not">not</option> + <option value="range">range</option> + </param> + <when value="equal"> + <param name="query_text" type="text" label="Searched term"/> + </when> + <when value="not"> + <param name="query_text" type="text" label="Searched term"/> + <param name="not_query_text" type="text" label="Limiting term"/> + </when> + <when value="range"> + <param name="min" type="text" label="From"/> + <param name="max" type="text" label="To"/> + </when> + </conditional> + </repeat> + </when> + + <when value="intact-interactions"> + <param name="fields" type="select" label="Fields to extract" multiple="true"> + <option value="AFCS" selected="true">AFCS</option> + <option value="BRENDA" selected="true">BRENDA</option> + <option value="CELL_ONTOLOGY" selected="true">CELL_ONTOLOGY</option> + <option value="CHEBI" selected="true">CHEBI</option> + <option value="CHEMBL_COMPOUND" selected="true">CHEMBL_COMPOUND</option> + <option value="EFO" selected="true">EFO</option> + <option value="EMDB" selected="true">EMDB</option> + <option value="FLANNOTATOR" selected="true">FLANNOTATOR</option> + <option value="GO" selected="true">GO</option> + <option value="IMEX" selected="true">IMEX</option> + <option value="INTACT" selected="true">INTACT</option> + <option value="INTACT.EXPERIMENT" selected="true">INTACT.EXPERIMENT</option> + <option value="INTACT.INTERACTOR" selected="true">INTACT.INTERACTOR</option> + <option value="INTENZ" selected="true">INTENZ</option> + <option value="INTERPRO" selected="true">INTERPRO</option> + <option value="MATRIXDB" selected="true">MATRIXDB</option> + <option value="MINT" selected="true">MINT</option> + <option value="OMIM" selected="true">OMIM</option> + <option value="PDBE" selected="true">PDBE</option> + <option value="PDBJ" selected="true">PDBJ</option> + <option value="PMC" selected="true">PMC</option> + <option value="PRIDE" selected="true">PRIDE</option> + <option value="PRINTS" selected="true">PRINTS</option> + <option value="PROTEOMEXCHANGE" selected="true">PROTEOMEXCHANGE</option> + <option value="PSI-MI" selected="true">PSI-MI</option> + <option value="PUBMED" selected="true">PUBMED</option> + <option value="RCSB_PDB" selected="true">RCSB_PDB</option> + <option value="REACTOME" selected="true">REACTOME</option> + <option value="SGD" selected="true">SGD</option> + <option value="UNIPROTKB" selected="true">UNIPROTKB</option> + <option value="WWPDB" selected="true">WWPDB</option> + <option value="description" selected="true">description</option> + <option value="domain_source" selected="true">domain_source</option> + <option value="id" selected="true">id</option> + <option value="name" selected="true">name</option> + <validator type="no_options" message="Please select at least one field" /> + </param> + <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> + <param name="query_field" type="select" label="Fields" > + <option value="AFCS">AFCS</option> + <option value="BRENDA">BRENDA</option> + <option value="CELL_ONTOLOGY">CELL_ONTOLOGY</option> + <option value="CHEBI">CHEBI</option> + <option value="CHEMBL_COMPOUND">CHEMBL_COMPOUND</option> + <option value="EFO">EFO</option> + <option value="EMDB">EMDB</option> + <option value="FLANNOTATOR">FLANNOTATOR</option> + <option value="GO">GO</option> + <option value="IMEX">IMEX</option> + <option value="INTACT">INTACT</option> + <option value="INTACT.EXPERIMENT">INTACT.EXPERIMENT</option> + <option value="INTACT.INTERACTOR">INTACT.INTERACTOR</option> + <option value="INTENZ">INTENZ</option> + <option value="INTERPRO">INTERPRO</option> + <option value="MATRIXDB">MATRIXDB</option> + <option value="MINT">MINT</option> + <option value="MPIDB">MPIDB</option> + <option value="OMIM">OMIM</option> + <option value="PDBE">PDBE</option> + <option value="PDBJ">PDBJ</option> + <option value="PMC">PMC</option> + <option value="PRIDE">PRIDE</option> + <option value="PRINTS">PRINTS</option> + <option value="PROTEOMEXCHANGE">PROTEOMEXCHANGE</option> + <option value="PSI-MI">PSI-MI</option> + <option value="PUBMED">PUBMED</option> + <option value="RCSB_PDB">RCSB_PDB</option> + <option value="REACTOME">REACTOME</option> + <option value="SGD">SGD</option> + <option value="UNIPROTKB">UNIPROTKB</option> + <option value="WWPDB">WWPDB</option> + <option value="creation_date">creation_date</option> + <option value="description">description</option> + <option value="domain_source">domain_source</option> + <option value="id">id</option> + <option value="interaction_detection_method">interaction_detection_method</option> + <option value="interaction_type">interaction_type</option> + <option value="last_modification_date">last_modification_date</option> + <option value="name">name</option> + <option value="participant_detection_method">participant_detection_method</option> + </param> + <conditional name="comp_operation"> + <param name="operation" type="select" label="Comparison operation" > + <option value="equal">equal</option> + <option value="not">not</option> + <option value="range">range</option> + </param> + <when value="equal"> + <param name="query_text" type="text" label="Searched term"/> + </when> + <when value="not"> + <param name="query_text" type="text" label="Searched term"/> + <param name="not_query_text" type="text" label="Limiting term"/> + </when> + <when value="range"> + <param name="min" type="text" label="From"/> + <param name="max" type="text" label="To"/> + </when> + </conditional> + </repeat> + </when> + + <when value="intact-interactors"> + <param name="fields" type="select" label="Fields to extract" multiple="true"> + <option value="AFCS" selected="true">AFCS</option> + <option value="CAMJEDB" selected="true">CAMJEDB</option> + <option value="CAS_REGISTRY_NUMBER" selected="true">CAS_REGISTRY_NUMBER</option> + <option value="CHEBI" selected="true">CHEBI</option> + <option value="CHEMBL" selected="true">CHEMBL</option> + <option value="CHEMBL_COMPOUND" selected="true">CHEMBL_COMPOUND</option> + <option value="CHEMBL_TARGET" selected="true">CHEMBL_TARGET</option> + <option value="CYGD" selected="true">CYGD</option> + <option value="DDBJ_EMBL_GENBANK" selected="true">DDBJ_EMBL_GENBANK</option> + <option value="DICTYBASE" selected="true">DICTYBASE</option> + <option value="EFO" selected="true">EFO</option> + <option value="EMDB" selected="true">EMDB</option> + <option value="ENSEMBL" selected="true">ENSEMBL</option> + <option value="ENSEMBLGENOMES" selected="true">ENSEMBLGENOMES</option> + <option value="ENTREZGENE_LOCUSLINK" selected="true">ENTREZGENE_LOCUSLINK</option> + <option value="EVIDENCE_ONTOLOGY" selected="true">EVIDENCE_ONTOLOGY</option> + <option value="FLANNOTATOR" selected="true">FLANNOTATOR</option> + <option value="FLYBASE" selected="true">FLYBASE</option> + <option value="GENBANK_INDENTIFIER" selected="true">GENBANK_INDENTIFIER</option> + <option value="GENBANK_NUCL_GI" selected="true">GENBANK_NUCL_GI</option> + <option value="GENBANK_PROTEIN_GI" selected="true">GENBANK_PROTEIN_GI</option> + <option value="GO" selected="true">GO</option> + <option value="HUMAN_GENOME_NOMENCLATURE_COMMITTEE" selected="true">HUMAN_GENOME_NOMENCLATURE_COMMITTEE</option> + <option value="IMEX" selected="true">IMEX</option> + <option value="INTACT" selected="true">INTACT</option> + <option value="INTACT.COMPLEX" selected="true">INTACT.COMPLEX</option> + <option value="INTACT.EXPERIMENT" selected="true">INTACT.EXPERIMENT</option> + <option value="INTACT.INTERACTION" selected="true">INTACT.INTERACTION</option> + <option value="INTENZ" selected="true">INTENZ</option> + <option value="INTERPRO" selected="true">INTERPRO</option> + <option value="IPI" selected="true">IPI</option> + <option value="MATRIXDB" selected="true">MATRIXDB</option> + <option value="MINT" selected="true">MINT</option> + <option value="MIRBASE" selected="true">MIRBASE</option> + <option value="PDBE" selected="true">PDBE</option> + <option value="PROTEIN_ONTOLOGY" selected="true">PROTEIN_ONTOLOGY</option> + <option value="PSI-MI" selected="true">PSI-MI</option> + <option value="PUBCHEM" selected="true">PUBCHEM</option> + <option value="PUBMED" selected="true">PUBMED</option> + <option value="RCSB_PDB" selected="true">RCSB_PDB</option> + <option value="REACTOME" selected="true">REACTOME</option> + <option value="REFSEQ" selected="true">REFSEQ</option> + <option value="RGD" selected="true">RGD</option> + <option value="RNACENTRAL" selected="true">RNACENTRAL</option> + <option value="SGD" selected="true">SGD</option> + <option value="TAIR" selected="true">TAIR</option> + <option value="UNIPARC" selected="true">UNIPARC</option> + <option value="UNIPROTKB" selected="true">UNIPROTKB</option> + <option value="WORMBASE" selected="true">WORMBASE</option> + <option value="WWPDB" selected="true">WWPDB</option> + <option value="description" selected="true">description</option> + <option value="domain_source" selected="true">domain_source</option> + <option value="id" selected="true">id</option> + <option value="name" selected="true">name</option> + <validator type="no_options" message="Please select at least one field" /> + </param> + <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> + <param name="query_field" type="select" label="Fields" > + <option value="AFCS">AFCS</option> + <option value="BIND_SMID">BIND_SMID</option> + <option value="CAMJEDB">CAMJEDB</option> + <option value="CAS_REGISTRY_NUMBER">CAS_REGISTRY_NUMBER</option> + <option value="CHEBI">CHEBI</option> + <option value="CHEMBL">CHEMBL</option> + <option value="CHEMBL_COMPOUND">CHEMBL_COMPOUND</option> + <option value="CHEMBL_TARGET">CHEMBL_TARGET</option> + <option value="CYGD">CYGD</option> + <option value="DDBJ_EMBL_GENBANK">DDBJ_EMBL_GENBANK</option> + <option value="DICTYBASE">DICTYBASE</option> + <option value="EFO">EFO</option> + <option value="EMDB">EMDB</option> + <option value="ENSEMBL">ENSEMBL</option> + <option value="ENSEMBLGENOMES">ENSEMBLGENOMES</option> + <option value="ENTREZGENE_LOCUSLINK">ENTREZGENE_LOCUSLINK</option> + <option value="EVIDENCE_ONTOLOGY">EVIDENCE_ONTOLOGY</option> + <option value="FLANNOTATOR">FLANNOTATOR</option> + <option value="FLYBASE">FLYBASE</option> + <option value="GENBANK_INDENTIFIER">GENBANK_INDENTIFIER</option> + <option value="GENBANK_NUCL_GI">GENBANK_NUCL_GI</option> + <option value="GENBANK_PROTEIN_GI">GENBANK_PROTEIN_GI</option> + <option value="GO">GO</option> + <option value="HUMAN_GENOME_NOMENCLATURE_COMMITTEE">HUMAN_GENOME_NOMENCLATURE_COMMITTEE</option> + <option value="IMEX">IMEX</option> + <option value="INTACT">INTACT</option> + <option value="INTACT.COMPLEX">INTACT.COMPLEX</option> + <option value="INTACT.EXPERIMENT">INTACT.EXPERIMENT</option> + <option value="INTACT.INTERACTION">INTACT.INTERACTION</option> + <option value="INTENZ">INTENZ</option> + <option value="INTERPRO">INTERPRO</option> + <option value="IPI">IPI</option> + <option value="MATRIXDB">MATRIXDB</option> + <option value="MINT">MINT</option> + <option value="MIRBASE">MIRBASE</option> + <option value="PDBE">PDBE</option> + <option value="PROTEIN_ONTOLOGY">PROTEIN_ONTOLOGY</option> + <option value="PSI-MI">PSI-MI</option> + <option value="PUBCHEM">PUBCHEM</option> + <option value="PUBMED">PUBMED</option> + <option value="RCSB_PDB">RCSB_PDB</option> + <option value="REACTOME">REACTOME</option> + <option value="REFSEQ">REFSEQ</option> + <option value="RGD">RGD</option> + <option value="RNACENTRAL">RNACENTRAL</option> + <option value="SGD">SGD</option> + <option value="TAIR">TAIR</option> + <option value="UNIPARC">UNIPARC</option> + <option value="UNIPROTKB">UNIPROTKB</option> + <option value="WORMBASE">WORMBASE</option> + <option value="WWPDB">WWPDB</option> + <option value="author_assigned_name">author_assigned_name</option> + <option value="complex_recommended_name">complex_recommended_name</option> + <option value="complex_synonym">complex_synonym</option> + <option value="complex_systematic_name">complex_systematic_name</option> + <option value="creation_date">creation_date</option> + <option value="description">description</option> + <option value="domain_source">domain_source</option> + <option value="gene_name">gene_name</option> + <option value="gene_name_synonym">gene_name_synonym</option> + <option value="id">id</option> + <option value="interaction_detection_method">interaction_detection_method</option> + <option value="interaction_type">interaction_type</option> + <option value="isoform_synonym">isoform_synonym</option> + <option value="iupac_name">iupac_name</option> + <option value="last_modification_date">last_modification_date</option> + <option value="locus_name">locus_name</option> + <option value="name">name</option> + <option value="orf_name">orf_name</option> + <option value="participant_detection_method">participant_detection_method</option> + <option value="synonym">synonym</option> + </param> + <conditional name="comp_operation"> + <param name="operation" type="select" label="Comparison operation" > + <option value="equal">equal</option> + <option value="not">not</option> + <option value="range">range</option> + </param> + <when value="equal"> + <param name="query_text" type="text" label="Searched term"/> + </when> + <when value="not"> + <param name="query_text" type="text" label="Searched term"/> + <param name="not_query_text" type="text" label="Limiting term"/> + </when> + <when value="range"> + <param name="min" type="text" label="From"/> + <param name="max" type="text" label="To"/> + </when> + </conditional> + </repeat> + </when> + + <when value="intenz"> + <param name="fields" type="select" label="Fields to extract" multiple="true"> + <option value="CAS" selected="true">CAS</option> + <option value="CHEBI" selected="true">CHEBI</option> + <option value="EC" selected="true">EC</option> + <option value="GO" selected="true">GO</option> + <option value="MEROPS" selected="true">MEROPS</option> + <option value="PROSITE" selected="true">PROSITE</option> + <option value="PUBMED" selected="true">PUBMED</option> + <option value="RHEA" selected="true">RHEA</option> + <option value="UNIPROT" selected="true">UNIPROT</option> + <option value="acc" selected="true">acc</option> + <option value="description" selected="true">description</option> + <option value="domain_source" selected="true">domain_source</option> + <option value="id" selected="true">id</option> + <option value="name" selected="true">name</option> + <validator type="no_options" message="Please select at least one field" /> + </param> + <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> + <param name="query_field" type="select" label="Fields" > + <option value="CAS">CAS</option> + <option value="CHEBI">CHEBI</option> + <option value="EC">EC</option> + <option value="GO">GO</option> + <option value="MEROPS">MEROPS</option> + <option value="PROSITE">PROSITE</option> + <option value="PUBMED">PUBMED</option> + <option value="RHEA">RHEA</option> + <option value="UNIPROT">UNIPROT</option> + <option value="acc">acc</option> + <option value="comment">comment</option> + <option value="description">description</option> + <option value="domain_source">domain_source</option> + <option value="id">id</option> + <option value="medline">medline</option> + <option value="name">name</option> + <option value="reaction">reaction</option> + <option value="reference">reference</option> + <option value="synonym">synonym</option> + <option value="systematic_name">systematic_name</option> + </param> + <conditional name="comp_operation"> + <param name="operation" type="select" label="Comparison operation" > + <option value="equal">equal</option> + <option value="not">not</option> + <option value="range">range</option> + </param> + <when value="equal"> + <param name="query_text" type="text" label="Searched term"/> + </when> + <when value="not"> + <param name="query_text" type="text" label="Searched term"/> + <param name="not_query_text" type="text" label="Limiting term"/> + </when> + <when value="range"> + <param name="min" type="text" label="From"/> + <param name="max" type="text" label="To"/> + </when> + </conditional> + </repeat> + </when> + + <when value="interpro"> + <param name="fields" type="select" label="Fields to extract" multiple="true"> + <option value="CATH" selected="true">CATH</option> + <option value="CAZY" selected="true">CAZY</option> + <option value="CDD" selected="true">CDD</option> + <option value="COME" selected="true">COME</option> + <option value="EC" selected="true">EC</option> + <option value="ENZYME" selected="true">ENZYME</option> + <option value="GENE3D" selected="true">GENE3D</option> + <option value="GO" selected="true">GO</option> + <option value="HAMAP" selected="true">HAMAP</option> + <option value="INTERPRO_PARENT" selected="true">INTERPRO_PARENT</option> + <option value="IUPHAR_RECEPTOR_CODE" selected="true">IUPHAR_RECEPTOR_CODE</option> + <option value="PANDIT" selected="true">PANDIT</option> + <option value="PANTHER" selected="true">PANTHER</option> + <option value="PDB" selected="true">PDB</option> + <option value="PDBSITE" selected="true">PDBSITE</option> + <option value="PFAM" selected="true">PFAM</option> + <option value="PFAM_SN" selected="true">PFAM_SN</option> + <option value="PIRSF" selected="true">PIRSF</option> + <option value="PRIAM" selected="true">PRIAM</option> + <option value="PRINTS" selected="true">PRINTS</option> + <option value="PRODOM" selected="true">PRODOM</option> + <option value="PROSITE" selected="true">PROSITE</option> + <option value="PROSITE_DOC" selected="true">PROSITE_DOC</option> + <option value="PROSITE_PATTERNS" selected="true">PROSITE_PATTERNS</option> + <option value="PUBMED" selected="true">PUBMED</option> + <option value="SCOP" selected="true">SCOP</option> + <option value="SFLD" selected="true">SFLD</option> + <option value="SMART" selected="true">SMART</option> + <option value="SUPERFAMILY" selected="true">SUPERFAMILY</option> + <option value="TIGRFAMS" selected="true">TIGRFAMS</option> + <option value="UNIPROT" selected="true">UNIPROT</option> + <option value="description" selected="true">description</option> + <option value="domain_source" selected="true">domain_source</option> + <option value="id" selected="true">id</option> + <option value="name" selected="true">name</option> + <option value="type" selected="true">type</option> + <validator type="no_options" message="Please select at least one field" /> + </param> + <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> + <param name="query_field" type="select" label="Fields" > + <option value="CATH">CATH</option> + <option value="CAZY">CAZY</option> + <option value="CDD">CDD</option> + <option value="CDD_SN">CDD_SN</option> + <option value="COME">COME</option> + <option value="EC">EC</option> + <option value="ENZYME">ENZYME</option> + <option value="GENE3D">GENE3D</option> + <option value="GENE3D_SN">GENE3D_SN</option> + <option value="GO">GO</option> + <option value="HAMAP">HAMAP</option> + <option value="HAMAP_SN">HAMAP_SN</option> + <option value="INTERPRO_PARENT">INTERPRO_PARENT</option> + <option value="IUPHAR_RECEPTOR_CODE">IUPHAR_RECEPTOR_CODE</option> + <option value="PANDIT">PANDIT</option> + <option value="PANTHER">PANTHER</option> + <option value="PANTHER_SN">PANTHER_SN</option> + <option value="PDB">PDB</option> + <option value="PDBSITE">PDBSITE</option> + <option value="PFAM">PFAM</option> + <option value="PFAM_SN">PFAM_SN</option> + <option value="PIRSF">PIRSF</option> + <option value="PIRSF_SN">PIRSF_SN</option> + <option value="PRIAM">PRIAM</option> + <option value="PRINTS">PRINTS</option> + <option value="PRINTS_SN">PRINTS_SN</option> + <option value="PRODOM">PRODOM</option> + <option value="PRODOM_SN">PRODOM_SN</option> + <option value="PROFILE_SN">PROFILE_SN</option> + <option value="PROSITE">PROSITE</option> + <option value="PROSITE_DOC">PROSITE_DOC</option> + <option value="PROSITE_PATTERNS">PROSITE_PATTERNS</option> + <option value="PROSITE_SN">PROSITE_SN</option> + <option value="PUBMED">PUBMED</option> + <option value="SCOP">SCOP</option> + <option value="SFLD">SFLD</option> + <option value="SFLD_SN">SFLD_SN</option> + <option value="SMART">SMART</option> + <option value="SMART_SN">SMART_SN</option> + <option value="SSF_SN">SSF_SN</option> + <option value="SUPERFAMILY">SUPERFAMILY</option> + <option value="TIGRFAMS">TIGRFAMS</option> + <option value="TIGRFAMS_SN">TIGRFAMS_SN</option> + <option value="UNIPROT">UNIPROT</option> + <option value="description">description</option> + <option value="domain_source">domain_source</option> + <option value="id">id</option> + <option value="name">name</option> + <option value="short_name">short_name</option> + <option value="type">type</option> + </param> + <conditional name="comp_operation"> + <param name="operation" type="select" label="Comparison operation" > + <option value="equal">equal</option> + <option value="not">not</option> + <option value="range">range</option> + </param> + <when value="equal"> + <param name="query_text" type="text" label="Searched term"/> + </when> + <when value="not"> + <param name="query_text" type="text" label="Searched term"/> + <param name="not_query_text" type="text" label="Limiting term"/> + </when> + <when value="range"> + <param name="min" type="text" label="From"/> + <param name="max" type="text" label="To"/> + </when> + </conditional> + </repeat> + </when> + + <when value="iprmatches"> + <param name="fields" type="select" label="Fields to extract" multiple="true"> + <option value="CDD" selected="true">CDD</option> + <option value="GENE3D" selected="true">GENE3D</option> + <option value="HAMAP" selected="true">HAMAP</option> + <option value="INTERPRO" selected="true">INTERPRO</option> + <option value="MOBIDBLT" selected="true">MOBIDBLT</option> + <option value="PANTHER" selected="true">PANTHER</option> + <option value="PFAM" selected="true">PFAM</option> + <option value="PIRSF" selected="true">PIRSF</option> + <option value="PRINTS" selected="true">PRINTS</option> + <option value="PRODOM" selected="true">PRODOM</option> + <option value="PROFILE" selected="true">PROFILE</option> + <option value="PROSITE" selected="true">PROSITE</option> + <option value="SFLD" selected="true">SFLD</option> + <option value="SMART" selected="true">SMART</option> + <option value="SSF" selected="true">SSF</option> + <option value="TIGRFAMS" selected="true">TIGRFAMS</option> + <option value="UNIPROT" selected="true">UNIPROT</option> + <option value="domain_source" selected="true">domain_source</option> + <option value="id" selected="true">id</option> + <option value="name" selected="true">name</option> + <validator type="no_options" message="Please select at least one field" /> + </param> + <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> + <param name="query_field" type="select" label="Fields" > + <option value="CDD">CDD</option> + <option value="GENE3D">GENE3D</option> + <option value="HAMAP">HAMAP</option> + <option value="INTERPRO">INTERPRO</option> + <option value="MOBIDBLT">MOBIDBLT</option> + <option value="PANTHER">PANTHER</option> + <option value="PFAM">PFAM</option> + <option value="PIRSF">PIRSF</option> + <option value="PRINTS">PRINTS</option> + <option value="PRODOM">PRODOM</option> + <option value="PROFILE">PROFILE</option> + <option value="PROSITE">PROSITE</option> + <option value="SFLD">SFLD</option> + <option value="SMART">SMART</option> + <option value="SSF">SSF</option> + <option value="TIGRFAMS">TIGRFAMS</option> + <option value="UNIPROT">UNIPROT</option> + <option value="domain_source">domain_source</option> + <option value="id">id</option> + <option value="name">name</option> + <option value="signatureName">signatureName</option> + </param> + <conditional name="comp_operation"> + <param name="operation" type="select" label="Comparison operation" > + <option value="equal">equal</option> + <option value="not">not</option> + <option value="range">range</option> + </param> + <when value="equal"> + <param name="query_text" type="text" label="Searched term"/> + </when> + <when value="not"> + <param name="query_text" type="text" label="Searched term"/> + <param name="not_query_text" type="text" label="Limiting term"/> + </when> + <when value="range"> + <param name="min" type="text" label="From"/> + <param name="max" type="text" label="To"/> + </when> + </conditional> + </repeat> + </when> + + <when value="jpo"> + <param name="fields" type="select" label="Fields to extract" multiple="true"> + <option value="PATENT_NUMBER" selected="true">PATENT_NUMBER</option> + <option value="TAXON" selected="true">TAXON</option> + <option value="acc" selected="true">acc</option> + <option value="description" selected="true">description</option> + <option value="doc_file" selected="true">doc_file</option> + <option value="domain_source" selected="true">domain_source</option> + <option value="id" selected="true">id</option> + <option value="offset_end" selected="true">offset_end</option> + <option value="offset_start" selected="true">offset_start</option> + <validator type="no_options" message="Please select at least one field" /> + </param> + <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> + <param name="query_field" type="select" label="Fields" > + <option value="PATENT_NUMBER">PATENT_NUMBER</option> + <option value="TAXON">TAXON</option> + <option value="acc">acc</option> + <option value="creation_date">creation_date</option> + <option value="data_class">data_class</option> + <option value="description">description</option> + <option value="domain_source">domain_source</option> + <option value="id">id</option> + <option value="keywords">keywords</option> + <option value="length">length</option> + <option value="md5">md5</option> + <option value="organism">organism</option> + <option value="organism_classification">organism_classification</option> + <option value="organism_species">organism_species</option> + <option value="references">references</option> + </param> + <conditional name="comp_operation"> + <param name="operation" type="select" label="Comparison operation" > + <option value="equal">equal</option> + <option value="not">not</option> + <option value="range">range</option> + </param> + <when value="equal"> + <param name="query_text" type="text" label="Searched term"/> + </when> + <when value="not"> + <param name="query_text" type="text" label="Searched term"/> + <param name="not_query_text" type="text" label="Limiting term"/> + </when> + <when value="range"> + <param name="min" type="text" label="From"/> + <param name="max" type="text" label="To"/> + </when> + </conditional> + </repeat> + </when> + + <when value="kipo"> + <param name="fields" type="select" label="Fields to extract" multiple="true"> + <option value="PATENT_NUMBER" selected="true">PATENT_NUMBER</option> + <option value="TAXON" selected="true">TAXON</option> + <option value="acc" selected="true">acc</option> + <option value="description" selected="true">description</option> + <option value="doc_file" selected="true">doc_file</option> + <option value="domain_source" selected="true">domain_source</option> + <option value="id" selected="true">id</option> + <option value="offset_end" selected="true">offset_end</option> + <option value="offset_start" selected="true">offset_start</option> + <validator type="no_options" message="Please select at least one field" /> + </param> + <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> + <param name="query_field" type="select" label="Fields" > + <option value="PATENT_NUMBER">PATENT_NUMBER</option> + <option value="TAXON">TAXON</option> + <option value="acc">acc</option> + <option value="creation_date">creation_date</option> + <option value="data_class">data_class</option> + <option value="description">description</option> + <option value="domain_source">domain_source</option> + <option value="id">id</option> + <option value="keywords">keywords</option> + <option value="length">length</option> + <option value="md5">md5</option> + <option value="organism">organism</option> + <option value="organism_classification">organism_classification</option> + <option value="organism_species">organism_species</option> + <option value="references">references</option> + </param> + <conditional name="comp_operation"> + <param name="operation" type="select" label="Comparison operation" > + <option value="equal">equal</option> + <option value="not">not</option> + <option value="range">range</option> + </param> + <when value="equal"> + <param name="query_text" type="text" label="Searched term"/> + </when> + <when value="not"> + <param name="query_text" type="text" label="Searched term"/> + <param name="not_query_text" type="text" label="Limiting term"/> + </when> + <when value="range"> + <param name="min" type="text" label="From"/> + <param name="max" type="text" label="To"/> + </when> + </conditional> + </repeat> + </when> + + <when value="lrg"> + <param name="fields" type="select" label="Fields to extract" multiple="true"> + <option value="CCDS" selected="true">CCDS</option> + <option value="ENSEMBL" selected="true">ENSEMBL</option> + <option value="GENEID" selected="true">GENEID</option> + <option value="GI" selected="true">GI</option> + <option value="HGNC" selected="true">HGNC</option> + <option value="MIM" selected="true">MIM</option> + <option value="MIRBASE" selected="true">MIRBASE</option> + <option value="REFSEQ" selected="true">REFSEQ</option> + <option value="RFAM" selected="true">RFAM</option> + <option value="TAXONOMY" selected="true">TAXONOMY</option> + <option value="UNIPROTKB" selected="true">UNIPROTKB</option> + <option value="assembly" selected="true">assembly</option> + <option value="assembly_grch37" selected="true">assembly_grch37</option> + <option value="assembly_grch38" selected="true">assembly_grch38</option> + <option value="chr_end" selected="true">chr_end</option> + <option value="chr_end_grch37" selected="true">chr_end_grch37</option> + <option value="chr_end_grch38" selected="true">chr_end_grch38</option> + <option value="chr_name" selected="true">chr_name</option> + <option value="chr_name_grch37" selected="true">chr_name_grch37</option> + <option value="chr_name_grch38" selected="true">chr_name_grch38</option> + <option value="chr_start" selected="true">chr_start</option> + <option value="chr_start_grch37" selected="true">chr_start_grch37</option> + <option value="chr_start_grch38" selected="true">chr_start_grch38</option> + <option value="chr_strand" selected="true">chr_strand</option> + <option value="chr_strand_grch37" selected="true">chr_strand_grch37</option> + <option value="chr_strand_grch38" selected="true">chr_strand_grch38</option> + <option value="description" selected="true">description</option> + <option value="domain_source" selected="true">domain_source</option> + <option value="id" selected="true">id</option> + <option value="in_ensembl" selected="true">in_ensembl</option> + <option value="last_modification_date" selected="true">last_modification_date</option> + <option value="name" selected="true">name</option> + <option value="organism" selected="true">organism</option> + <option value="status" selected="true">status</option> + <option value="transcript_source" selected="true">transcript_source</option> + <validator type="no_options" message="Please select at least one field" /> + </param> + <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> + <param name="query_field" type="select" label="Fields" > + <option value="CCDS">CCDS</option> + <option value="ENSEMBL">ENSEMBL</option> + <option value="GENEID">GENEID</option> + <option value="GI">GI</option> + <option value="HGNC">HGNC</option> + <option value="MIM">MIM</option> + <option value="MIRBASE">MIRBASE</option> + <option value="REFSEQ">REFSEQ</option> + <option value="RFAM">RFAM</option> + <option value="TAXONOMY">TAXONOMY</option> + <option value="UNIPROTKB">UNIPROTKB</option> + <option value="creation_date">creation_date</option> + <option value="description">description</option> + <option value="domain_source">domain_source</option> + <option value="id">id</option> + <option value="in_ensembl">in_ensembl</option> + <option value="last_modification_date">last_modification_date</option> + <option value="name">name</option> + <option value="organism">organism</option> + <option value="status">status</option> + <option value="synonym">synonym</option> + </param> + <conditional name="comp_operation"> + <param name="operation" type="select" label="Comparison operation" > + <option value="equal">equal</option> + <option value="not">not</option> + <option value="range">range</option> + </param> + <when value="equal"> + <param name="query_text" type="text" label="Searched term"/> + </when> + <when value="not"> + <param name="query_text" type="text" label="Searched term"/> + <param name="not_query_text" type="text" label="Limiting term"/> + </when> + <when value="range"> + <param name="min" type="text" label="From"/> + <param name="max" type="text" label="To"/> + </when> + </conditional> + </repeat> + </when> + + <when value="large-assembly"> + <param name="fields" type="select" label="Fields to extract" multiple="true"> + <option value="DOI" selected="true">DOI</option> + <option value="PUBMED" selected="true">PUBMED</option> + <option value="TAXON" selected="true">TAXON</option> + <option value="acc" selected="true">acc</option> + <option value="description" selected="true">description</option> + <option value="domain_source" selected="true">domain_source</option> + <option value="id" selected="true">id</option> + <validator type="no_options" message="Please select at least one field" /> + </param> + <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> + <param name="query_field" type="select" label="Fields" > + <option value="DOI">DOI</option> + <option value="MD5">MD5</option> + <option value="PROJECT">PROJECT</option> + <option value="PUBMED">PUBMED</option> + <option value="TAXON">TAXON</option> + <option value="acc">acc</option> + <option value="creation_date">creation_date</option> + <option value="data_class">data_class</option> + <option value="description">description</option> + <option value="division">division</option> + <option value="domain_source">domain_source</option> + <option value="id">id</option> + <option value="keywords">keywords</option> + <option value="last_modification_date">last_modification_date</option> + <option value="length">length</option> + <option value="molecule_type">molecule_type</option> + <option value="organism">organism</option> + <option value="organism_classification">organism_classification</option> + <option value="organism_species">organism_species</option> + <option value="references">references</option> + <option value="sequence_version">sequence_version</option> + <option value="topology">topology</option> + </param> + <conditional name="comp_operation"> + <param name="operation" type="select" label="Comparison operation" > + <option value="equal">equal</option> + <option value="not">not</option> + <option value="range">range</option> + </param> + <when value="equal"> + <param name="query_text" type="text" label="Searched term"/> + </when> + <when value="not"> + <param name="query_text" type="text" label="Searched term"/> + <param name="not_query_text" type="text" label="Limiting term"/> + </when> + <when value="range"> + <param name="min" type="text" label="From"/> + <param name="max" type="text" label="To"/> + </when> + </conditional> + </repeat> + </when> + + <when value="pdbechem"> + <param name="fields" type="select" label="Fields to extract" multiple="true"> + <option value="acc" selected="true">acc</option> + <option value="description" selected="true">description</option> + <option value="domain_source" selected="true">domain_source</option> + <option value="id" selected="true">id</option> + <validator type="no_options" message="Please select at least one field" /> + </param> + <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> + <param name="query_field" type="select" label="Fields" > + <option value="acc">acc</option> + <option value="comp_synonyms">comp_synonyms</option> + <option value="description">description</option> + <option value="domain_source">domain_source</option> + <option value="formula">formula</option> + <option value="id">id</option> + <option value="inchi">inchi</option> + <option value="non_stereo_smiles">non_stereo_smiles</option> + <option value="stereo_smiles">stereo_smiles</option> + <option value="systematic_name">systematic_name</option> + <option value="weight">weight</option> + </param> + <conditional name="comp_operation"> + <param name="operation" type="select" label="Comparison operation" > + <option value="equal">equal</option> + <option value="not">not</option> + <option value="range">range</option> + </param> + <when value="equal"> + <param name="query_text" type="text" label="Searched term"/> + </when> + <when value="not"> + <param name="query_text" type="text" label="Searched term"/> + <param name="not_query_text" type="text" label="Limiting term"/> + </when> + <when value="range"> + <param name="min" type="text" label="From"/> + <param name="max" type="text" label="To"/> + </when> + </conditional> + </repeat> + </when> + + <when value="medline"> + <param name="fields" type="select" label="Fields to extract" multiple="true"> + <option value="MESH_DESCRIPTOR_NAME" selected="true">MESH_DESCRIPTOR_NAME</option> + <option value="ORCID" selected="true">ORCID</option> + <option value="author" selected="true">author</option> + <option value="description" selected="true">description</option> + <option value="display_author" selected="true">display_author</option> + <option value="display_publication_date" selected="true">display_publication_date</option> + <option value="domain_source" selected="true">domain_source</option> + <option value="id" selected="true">id</option> + <option value="issue" selected="true">issue</option> + <option value="journal" selected="true">journal</option> + <option value="name" selected="true">name</option> + <option value="pagination" selected="true">pagination</option> + <option value="publication_date" selected="true">publication_date</option> + <option value="volume" selected="true">volume</option> + <validator type="no_options" message="Please select at least one field" /> + </param> + <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> + <param name="query_field" type="select" label="Fields" > + <option value="MESH_DESCRIPTOR_NAME">MESH_DESCRIPTOR_NAME</option> + <option value="ORCID">ORCID</option> + <option value="affiliation">affiliation</option> + <option value="author">author</option> + <option value="creation_date">creation_date</option> + <option value="description">description</option> + <option value="display_publication_date">display_publication_date</option> + <option value="domain_source">domain_source</option> + <option value="id">id</option> + <option value="issn">issn</option> + <option value="issue">issue</option> + <option value="journal">journal</option> + <option value="keywords">keywords</option> + <option value="last_modification_date">last_modification_date</option> + <option value="mesh_qualifier_name">mesh_qualifier_name</option> + <option value="name">name</option> + <option value="pagination">pagination</option> + <option value="publication_date">publication_date</option> + <option value="volume">volume</option> + </param> + <conditional name="comp_operation"> + <param name="operation" type="select" label="Comparison operation" > + <option value="equal">equal</option> + <option value="not">not</option> + <option value="range">range</option> + </param> + <when value="equal"> + <param name="query_text" type="text" label="Searched term"/> + </when> + <when value="not"> + <param name="query_text" type="text" label="Searched term"/> + <param name="not_query_text" type="text" label="Limiting term"/> + </when> + <when value="range"> + <param name="min" type="text" label="From"/> + <param name="max" type="text" label="To"/> + </when> + </conditional> + </repeat> + </when> + + <when value="merops_clan"> + <param name="fields" type="select" label="Fields to extract" multiple="true"> + <option value="PFAM" selected="true">PFAM</option> + <option value="SCOP" selected="true">SCOP</option> + <option value="description" selected="true">description</option> + <option value="domain_source" selected="true">domain_source</option> + <option value="id" selected="true">id</option> + <option value="name" selected="true">name</option> + <validator type="no_options" message="Please select at least one field" /> + </param> + <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> + <param name="query_field" type="select" label="Fields" > + <option value="PFAM">PFAM</option> + <option value="SCOP">SCOP</option> + <option value="acc">acc</option> + <option value="activation_mechanism">activation_mechanism</option> + <option value="catalytic_mechanism">catalytic_mechanism</option> + <option value="content">content</option> + <option value="description">description</option> + <option value="distribution">distribution</option> + <option value="domain_source">domain_source</option> + <option value="evidence">evidence</option> + <option value="evolution">evolution</option> + <option value="homologous_nonpeptidase">homologous_nonpeptidase</option> + <option value="id">id</option> + <option value="inhibitors">inhibitors</option> + <option value="name">name</option> + <option value="peptidase_activity">peptidase_activity</option> + <option value="protein_fold">protein_fold</option> + <option value="published">published</option> + <option value="reviews">reviews</option> + <option value="subclans">subclans</option> + </param> + <conditional name="comp_operation"> + <param name="operation" type="select" label="Comparison operation" > + <option value="equal">equal</option> + <option value="not">not</option> + <option value="range">range</option> + </param> + <when value="equal"> + <param name="query_text" type="text" label="Searched term"/> + </when> + <when value="not"> + <param name="query_text" type="text" label="Searched term"/> + <param name="not_query_text" type="text" label="Limiting term"/> + </when> + <when value="range"> + <param name="min" type="text" label="From"/> + <param name="max" type="text" label="To"/> + </when> + </conditional> + </repeat> + </when> + + <when value="merops_family"> + <param name="fields" type="select" label="Fields to extract" multiple="true"> + <option value="CATH" selected="true">CATH</option> + <option value="HOMSTRAD" selected="true">HOMSTRAD</option> + <option value="HSSP" selected="true">HSSP</option> + <option value="INTERPRO" selected="true">INTERPRO</option> + <option value="MEROPS_CLAN" selected="true">MEROPS_CLAN</option> + <option value="PFAM" selected="true">PFAM</option> + <option value="SCOP" selected="true">SCOP</option> + <option value="description" selected="true">description</option> + <option value="domain_source" selected="true">domain_source</option> + <option value="id" selected="true">id</option> + <option value="name" selected="true">name</option> + <validator type="no_options" message="Please select at least one field" /> + </param> + <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> + <param name="query_field" type="select" label="Fields" > + <option value="CATH">CATH</option> + <option value="HOMSTRAD">HOMSTRAD</option> + <option value="HSSP">HSSP</option> + <option value="INTERPRO">INTERPRO</option> + <option value="MEROPS_CLAN">MEROPS_CLAN</option> + <option value="PFAM">PFAM</option> + <option value="SCOP">SCOP</option> + <option value="acc">acc</option> + <option value="active_site">active_site</option> + <option value="activities_and_specificities">activities_and_specificities</option> + <option value="biological_functions">biological_functions</option> + <option value="biotech_aspects">biotech_aspects</option> + <option value="clan_assignment">clan_assignment</option> + <option value="content">content</option> + <option value="description">description</option> + <option value="distribution">distribution</option> + <option value="domain_source">domain_source</option> + <option value="history">history</option> + <option value="id">id</option> + <option value="inhibitors">inhibitors</option> + <option value="mechanism">mechanism</option> + <option value="molecular_structure">molecular_structure</option> + <option value="name">name</option> + <option value="peptidases_inhibited">peptidases_inhibited</option> + <option value="published">published</option> + <option value="reactive_site">reactive_site</option> + <option value="reviews">reviews</option> + <option value="subfamilies">subfamilies</option> + </param> + <conditional name="comp_operation"> + <param name="operation" type="select" label="Comparison operation" > + <option value="equal">equal</option> + <option value="not">not</option> + <option value="range">range</option> + </param> + <when value="equal"> + <param name="query_text" type="text" label="Searched term"/> + </when> + <when value="not"> + <param name="query_text" type="text" label="Searched term"/> + <param name="not_query_text" type="text" label="Limiting term"/> + </when> + <when value="range"> + <param name="min" type="text" label="From"/> + <param name="max" type="text" label="To"/> + </when> + </conditional> + </repeat> + </when> + + <when value="merops_id"> + <param name="fields" type="select" label="Fields to extract" multiple="true"> + <option value="EMBL" selected="true">EMBL</option> + <option value="EMBLCDS" selected="true">EMBLCDS</option> + <option value="ENSEMBL" selected="true">ENSEMBL</option> + <option value="MEROPS_CLAN" selected="true">MEROPS_CLAN</option> + <option value="MEROPS_FAMILY" selected="true">MEROPS_FAMILY</option> + <option value="PDB" selected="true">PDB</option> + <option value="PIR" selected="true">PIR</option> + <option value="REFSEQ" selected="true">REFSEQ</option> + <option value="TAXONOMY" selected="true">TAXONOMY</option> + <option value="UNIPARC" selected="true">UNIPARC</option> + <option value="UNIPROT" selected="true">UNIPROT</option> + <option value="description" selected="true">description</option> + <option value="domain_source" selected="true">domain_source</option> + <option value="id" selected="true">id</option> + <option value="name" selected="true">name</option> + <validator type="no_options" message="Please select at least one field" /> + </param> + <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> + <param name="query_field" type="select" label="Fields" > + <option value="EMBL">EMBL</option> + <option value="EMBLCDS">EMBLCDS</option> + <option value="ENSEMBL">ENSEMBL</option> + <option value="MEROPS_CLAN">MEROPS_CLAN</option> + <option value="MEROPS_FAMILY">MEROPS_FAMILY</option> + <option value="PDB">PDB</option> + <option value="PIR">PIR</option> + <option value="REFSEQ">REFSEQ</option> + <option value="TAXONOMY">TAXONOMY</option> + <option value="UNIPARC">UNIPARC</option> + <option value="UNIPROT">UNIPROT</option> + <option value="acc">acc</option> + <option value="activity">activity</option> + <option value="biotech">biotech</option> + <option value="common_name">common_name</option> + <option value="description">description</option> + <option value="distinguishing_features">distinguishing_features</option> + <option value="domain_source">domain_source</option> + <option value="gene_name">gene_name</option> + <option value="history">history</option> + <option value="id">id</option> + <option value="id_noversion">id_noversion</option> + <option value="inhibitors">inhibitors</option> + <option value="knockout">knockout</option> + <option value="name">name</option> + <option value="other_name">other_name</option> + <option value="pharma">pharma</option> + <option value="physiology">physiology</option> + <option value="smi">smi</option> + <option value="species">species</option> + <option value="specificity">specificity</option> + <option value="structure">structure</option> + </param> + <conditional name="comp_operation"> + <param name="operation" type="select" label="Comparison operation" > + <option value="equal">equal</option> + <option value="not">not</option> + <option value="range">range</option> + </param> + <when value="equal"> + <param name="query_text" type="text" label="Searched term"/> + </when> + <when value="not"> + <param name="query_text" type="text" label="Searched term"/> + <param name="not_query_text" type="text" label="Limiting term"/> + </when> + <when value="range"> + <param name="min" type="text" label="From"/> + <param name="max" type="text" label="To"/> + </when> + </conditional> + </repeat> + </when> + + <when value="mesh"> + <param name="fields" type="select" label="Fields to extract" multiple="true"> + <option value="MESH_PHARMA" selected="true">MESH_PHARMA</option> + <option value="domain_source" selected="true">domain_source</option> + <option value="id" selected="true">id</option> + <option value="name" selected="true">name</option> + <validator type="no_options" message="Please select at least one field" /> + </param> + <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> + <param name="query_field" type="select" label="Fields" > + <option value="MESH_PHARMA">MESH_PHARMA</option> + <option value="annotation">annotation</option> + <option value="creation_date">creation_date</option> + <option value="domain_source">domain_source</option> + <option value="established_date">established_date</option> + <option value="historynote">historynote</option> + <option value="id">id</option> + <option value="last_modification_date">last_modification_date</option> + <option value="name">name</option> + <option value="onlinenote">onlinenote</option> + <option value="previousindexing">previousindexing</option> + <option value="publicmeshnote">publicmeshnote</option> + <option value="qualifierabbr">qualifierabbr</option> + <option value="qualifiername">qualifiername</option> + <option value="qualifierui">qualifierui</option> + </param> + <conditional name="comp_operation"> + <param name="operation" type="select" label="Comparison operation" > + <option value="equal">equal</option> + <option value="not">not</option> + <option value="range">range</option> + </param> + <when value="equal"> + <param name="query_text" type="text" label="Searched term"/> + </when> + <when value="not"> + <param name="query_text" type="text" label="Searched term"/> + <param name="not_query_text" type="text" label="Limiting term"/> + </when> + <when value="range"> + <param name="min" type="text" label="From"/> + <param name="max" type="text" label="To"/> + </when> + </conditional> + </repeat> + </when> + + <when value="massive"> + <param name="fields" type="select" label="Fields to extract" multiple="true"> + <option value="PUBMED" selected="true">PUBMED</option> + <option value="TAXONOMY" selected="true">TAXONOMY</option> + <option value="dataset_file" selected="true">dataset_file</option> + <option value="description" selected="true">description</option> + <option value="domain_source" selected="true">domain_source</option> + <option value="full_dataset_link" selected="true">full_dataset_link</option> + <option value="id" selected="true">id</option> + <option value="instrument_platform" selected="true">instrument_platform</option> + <option value="modification" selected="true">modification</option> + <option value="name" selected="true">name</option> + <option value="omics_type" selected="true">omics_type</option> + <option value="species" selected="true">species</option> + <option value="submission_date" selected="true">submission_date</option> + <option value="technology_type" selected="true">technology_type</option> + <validator type="no_options" message="Please select at least one field" /> + </param> + <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> + <param name="query_field" type="select" label="Fields" > + <option value="PUBMED">PUBMED</option> + <option value="TAXONOMY">TAXONOMY</option> + <option value="acc">acc</option> + <option value="curator_keywords">curator_keywords</option> + <option value="description">description</option> + <option value="description_synonyms">description_synonyms</option> + <option value="domain_source">domain_source</option> + <option value="full_dataset_link">full_dataset_link</option> + <option value="id">id</option> + <option value="instrument_platform">instrument_platform</option> + <option value="modification">modification</option> + <option value="name">name</option> + <option value="name_synonyms">name_synonyms</option> + <option value="omics_type">omics_type</option> + <option value="repository">repository</option> + <option value="species">species</option> + <option value="submission_date">submission_date</option> + <option value="submitter">submitter</option> + <option value="technology_type">technology_type</option> + </param> + <conditional name="comp_operation"> + <param name="operation" type="select" label="Comparison operation" > + <option value="equal">equal</option> + <option value="not">not</option> + <option value="range">range</option> + </param> + <when value="equal"> + <param name="query_text" type="text" label="Searched term"/> + </when> + <when value="not"> + <param name="query_text" type="text" label="Searched term"/> + <param name="not_query_text" type="text" label="Limiting term"/> + </when> + <when value="range"> + <param name="min" type="text" label="From"/> + <param name="max" type="text" label="To"/> + </when> + </conditional> + </repeat> + </when> + + <when value="metabolights"> + <param name="fields" type="select" label="Fields to extract" multiple="true"> + <option value="CHEBI" selected="true">CHEBI</option> + <option value="HMDB" selected="true">HMDB</option> + <option value="KEGG" selected="true">KEGG</option> + <option value="METABOLIGHTS" selected="true">METABOLIGHTS</option> + <option value="MTBLS" selected="true">MTBLS</option> + <option value="PUBCHEM" selected="true">PUBCHEM</option> + <option value="PUBMED" selected="true">PUBMED</option> + <option value="dataset_file" selected="true">dataset_file</option> + <option value="description" selected="true">description</option> + <option value="domain_source" selected="true">domain_source</option> + <option value="full_dataset_link" selected="true">full_dataset_link</option> + <option value="id" selected="true">id</option> + <option value="instrument_platform" selected="true">instrument_platform</option> + <option value="name" selected="true">name</option> + <option value="omics_type" selected="true">omics_type</option> + <option value="publication" selected="true">publication</option> + <option value="publication_date" selected="true">publication_date</option> + <option value="study_design" selected="true">study_design</option> + <option value="study_factor" selected="true">study_factor</option> + <option value="study_status" selected="true">study_status</option> + <option value="submission_date" selected="true">submission_date</option> + <option value="technology_type" selected="true">technology_type</option> + <validator type="no_options" message="Please select at least one field" /> + </param> + <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> + <param name="query_field" type="select" label="Fields" > + <option value="3d_desi_imaging_ms_dataset_of_a_human_colorectal_adenocarcinoma_protocol">3d_desi_imaging_ms_dataset_of_a_human_colorectal_adenocarcinoma_protocol</option> + <option value="3d_maldi_imaging_ms_dataset_of_a_human_oral_squamous_cell_carcinoma_protocol">3d_maldi_imaging_ms_dataset_of_a_human_oral_squamous_cell_carcinoma_protocol</option> + <option value="3d_maldi_imaging_ms_dataset_of_a_mouse_kidney_protocol">3d_maldi_imaging_ms_dataset_of_a_mouse_kidney_protocol</option> + <option value="3d_maldi_imaging_ms_dataset_of_a_mouse_pancreas_protocol">3d_maldi_imaging_ms_dataset_of_a_mouse_pancreas_protocol</option> + <option value="3d_maldi_imaging_ms_datasets_of_cultured_microbial_colonies_in_a_time_course_experiment_protocol">3d_maldi_imaging_ms_datasets_of_cultured_microbial_colonies_in_a_time_course_experiment_protocol</option> + <option value="CHEBI">CHEBI</option> + <option value="HMDB">HMDB</option> + <option value="KEGG">KEGG</option> + <option value="METABOLIGHTS">METABOLIGHTS</option> + <option value="MTBLS">MTBLS</option> + <option value="PUBCHEM">PUBCHEM</option> + <option value="PUBMED">PUBMED</option> + <option value="apodisation_zero_filling_and_fourier_transformation_protocol">apodisation_zero_filling_and_fourier_transformation_protocol</option> + <option value="author">author</option> + <option value="averaging_of_transients_protocol">averaging_of_transients_protocol</option> + <option value="batch_correction_protocol">batch_correction_protocol</option> + <option value="chromatography_protocol">chromatography_protocol</option> + <option value="data_analysis_protocol">data_analysis_protocol</option> + <option value="data_normalization_protocol">data_normalization_protocol</option> + <option value="data_transformation_protocol">data_transformation_protocol</option> + <option value="description">description</option> + <option value="domain_source">domain_source</option> + <option value="extraction_protocol">extraction_protocol</option> + <option value="formula">formula</option> + <option value="full_dataset_link">full_dataset_link</option> + <option value="gc_ms_protocol">gc_ms_protocol</option> + <option value="glog_transformation_protocol">glog_transformation_protocol</option> + <option value="growth_conditions_protocol">growth_conditions_protocol</option> + <option value="histology_protocol">histology_protocol</option> + <option value="id">id</option> + <option value="inchi">inchi</option> + <option value="instrument_platform">instrument_platform</option> + <option value="iupac">iupac</option> + <option value="labeling_protocol">labeling_protocol</option> + <option value="lc_ms_protocol">lc_ms_protocol</option> + <option value="mass_calibration_and_sim_stitching_protocol">mass_calibration_and_sim_stitching_protocol</option> + <option value="mass_spec_protocol">mass_spec_protocol</option> + <option value="metabolite_id_protocol">metabolite_id_protocol</option> + <option value="metabolite_name">metabolite_name</option> + <option value="missing_values_imputation__knn_protocol">missing_values_imputation__knn_protocol</option> + <option value="name">name</option> + <option value="nmr_assay_protocol">nmr_assay_protocol</option> + <option value="nmr_spec_protocol">nmr_spec_protocol</option> + <option value="omics_type">omics_type</option> + <option value="organism">organism</option> + <option value="organism_group">organism_group</option> + <option value="organism_part">organism_part</option> + <option value="pqn_normalisation_protocol">pqn_normalisation_protocol</option> + <option value="preparation_protocol">preparation_protocol</option> + <option value="publication">publication</option> + <option value="publication_date">publication_date</option> + <option value="replicate_filtering_protocol">replicate_filtering_protocol</option> + <option value="repository">repository</option> + <option value="sample_collection_protocol">sample_collection_protocol</option> + <option value="sample_filtering_including_tic_filtering_blank_filtering_and_missing_value_filtering_protocol">sample_filtering_including_tic_filtering_blank_filtering_and_missing_value_filtering_protocol</option> + <option value="software_processing_protocol">software_processing_protocol</option> + <option value="spectral_cleaning_protocol">spectral_cleaning_protocol</option> + <option value="study">study</option> + <option value="study_design">study_design</option> + <option value="study_factor">study_factor</option> + <option value="study_status">study_status</option> + <option value="submission_date">submission_date</option> + <option value="submitter">submitter</option> + <option value="submitter_affiliation">submitter_affiliation</option> + <option value="submitter_email">submitter_email</option> + <option value="technology_type">technology_type</option> + </param> + <conditional name="comp_operation"> + <param name="operation" type="select" label="Comparison operation" > + <option value="equal">equal</option> + <option value="not">not</option> + <option value="range">range</option> + </param> + <when value="equal"> + <param name="query_text" type="text" label="Searched term"/> + </when> + <when value="not"> + <param name="query_text" type="text" label="Searched term"/> + <param name="not_query_text" type="text" label="Limiting term"/> + </when> + <when value="range"> + <param name="min" type="text" label="From"/> + <param name="max" type="text" label="To"/> + </when> + </conditional> + </repeat> + </when> + + <when value="metabolights_dataset"> + <param name="fields" type="select" label="Fields to extract" multiple="true"> + <option value="CHEBI" selected="true">CHEBI</option> + <option value="HMDB" selected="true">HMDB</option> + <option value="KEGG" selected="true">KEGG</option> + <option value="METABOLIGHTS" selected="true">METABOLIGHTS</option> + <option value="PUBCHEM" selected="true">PUBCHEM</option> + <option value="PUBMED" selected="true">PUBMED</option> + <option value="dataset_file" selected="true">dataset_file</option> + <option value="description" selected="true">description</option> + <option value="domain_source" selected="true">domain_source</option> + <option value="full_dataset_link" selected="true">full_dataset_link</option> + <option value="id" selected="true">id</option> + <option value="instrument_platform" selected="true">instrument_platform</option> + <option value="name" selected="true">name</option> + <option value="omics_type" selected="true">omics_type</option> + <option value="publication" selected="true">publication</option> + <option value="publication_date" selected="true">publication_date</option> + <option value="study_design" selected="true">study_design</option> + <option value="study_factor" selected="true">study_factor</option> + <option value="study_status" selected="true">study_status</option> + <option value="submission_date" selected="true">submission_date</option> + <option value="technology_type" selected="true">technology_type</option> + <validator type="no_options" message="Please select at least one field" /> + </param> + <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> + <param name="query_field" type="select" label="Fields" > + <option value="3d_desi_imaging_ms_dataset_of_a_human_colorectal_adenocarcinoma_protocol">3d_desi_imaging_ms_dataset_of_a_human_colorectal_adenocarcinoma_protocol</option> + <option value="3d_maldi_imaging_ms_dataset_of_a_human_oral_squamous_cell_carcinoma_protocol">3d_maldi_imaging_ms_dataset_of_a_human_oral_squamous_cell_carcinoma_protocol</option> + <option value="3d_maldi_imaging_ms_dataset_of_a_mouse_kidney_protocol">3d_maldi_imaging_ms_dataset_of_a_mouse_kidney_protocol</option> + <option value="3d_maldi_imaging_ms_dataset_of_a_mouse_pancreas_protocol">3d_maldi_imaging_ms_dataset_of_a_mouse_pancreas_protocol</option> + <option value="3d_maldi_imaging_ms_datasets_of_cultured_microbial_colonies_in_a_time_course_experiment_protocol">3d_maldi_imaging_ms_datasets_of_cultured_microbial_colonies_in_a_time_course_experiment_protocol</option> + <option value="CHEBI">CHEBI</option> + <option value="HMDB">HMDB</option> + <option value="KEGG">KEGG</option> + <option value="METABOLIGHTS">METABOLIGHTS</option> + <option value="PUBCHEM">PUBCHEM</option> + <option value="PUBMED">PUBMED</option> + <option value="acc">acc</option> + <option value="apodisation_zero_filling_and_fourier_transformation_protocol">apodisation_zero_filling_and_fourier_transformation_protocol</option> + <option value="author">author</option> + <option value="averaging_of_transients_protocol">averaging_of_transients_protocol</option> + <option value="batch_correction_protocol">batch_correction_protocol</option> + <option value="chromatography_protocol">chromatography_protocol</option> + <option value="data_analysis_protocol">data_analysis_protocol</option> + <option value="data_normalization_protocol">data_normalization_protocol</option> + <option value="data_transformation_protocol">data_transformation_protocol</option> + <option value="derivatisation_protocol">derivatisation_protocol</option> + <option value="description">description</option> + <option value="description_synonyms">description_synonyms</option> + <option value="domain_source">domain_source</option> + <option value="extraction_protocol">extraction_protocol</option> + <option value="full_dataset_link">full_dataset_link</option> + <option value="gc_ms_protocol">gc_ms_protocol</option> + <option value="glog_transformation_protocol">glog_transformation_protocol</option> + <option value="growth_conditions_protocol">growth_conditions_protocol</option> + <option value="histology_protocol">histology_protocol</option> + <option value="id">id</option> + <option value="instrument_platform">instrument_platform</option> + <option value="labeling_protocol">labeling_protocol</option> + <option value="lc_ms_protocol">lc_ms_protocol</option> + <option value="mass_calibration_and_sim_stitching_protocol">mass_calibration_and_sim_stitching_protocol</option> + <option value="mass_spec_protocol">mass_spec_protocol</option> + <option value="metabolite_id_protocol">metabolite_id_protocol</option> + <option value="metabolite_name">metabolite_name</option> + <option value="missing_values_imputation__knn_protocol">missing_values_imputation__knn_protocol</option> + <option value="name">name</option> + <option value="name_synonyms">name_synonyms</option> + <option value="nmr_assay_protocol">nmr_assay_protocol</option> + <option value="nmr_spec_protocol">nmr_spec_protocol</option> + <option value="omics_type">omics_type</option> + <option value="organism">organism</option> + <option value="organism_part">organism_part</option> + <option value="pqn_normalisation_protocol">pqn_normalisation_protocol</option> + <option value="preparation_protocol">preparation_protocol</option> + <option value="publication">publication</option> + <option value="publication_date">publication_date</option> + <option value="pubmed_abstract">pubmed_abstract</option> + <option value="pubmed_abstract_synonyms">pubmed_abstract_synonyms</option> + <option value="pubmed_authors">pubmed_authors</option> + <option value="pubmed_title">pubmed_title</option> + <option value="pubmed_title_synonyms">pubmed_title_synonyms</option> + <option value="replicate_filtering_protocol">replicate_filtering_protocol</option> + <option value="repository">repository</option> + <option value="sample_collection_protocol">sample_collection_protocol</option> + <option value="sample_filtering_including_tic_filtering_blank_filtering_and_missing_value_filtering_protocol">sample_filtering_including_tic_filtering_blank_filtering_and_missing_value_filtering_protocol</option> + <option value="software_processing_protocol">software_processing_protocol</option> + <option value="spectral_cleaning_protocol">spectral_cleaning_protocol</option> + <option value="study_design">study_design</option> + <option value="study_factor">study_factor</option> + <option value="study_status">study_status</option> + <option value="submission_date">submission_date</option> + <option value="submitter">submitter</option> + <option value="submitter_affiliation">submitter_affiliation</option> + <option value="submitter_email">submitter_email</option> + <option value="technology_type">technology_type</option> + </param> + <conditional name="comp_operation"> + <param name="operation" type="select" label="Comparison operation" > + <option value="equal">equal</option> + <option value="not">not</option> + <option value="range">range</option> + </param> + <when value="equal"> + <param name="query_text" type="text" label="Searched term"/> + </when> + <when value="not"> + <param name="query_text" type="text" label="Searched term"/> + <param name="not_query_text" type="text" label="Limiting term"/> + </when> + <when value="range"> + <param name="min" type="text" label="From"/> + <param name="max" type="text" label="To"/> + </when> + </conditional> + </repeat> + </when> + + <when value="metabolome_express"> + <param name="fields" type="select" label="Fields to extract" multiple="true"> + <option value="CHEBI" selected="true">CHEBI</option> + <option value="PUBMED" selected="true">PUBMED</option> + <option value="description" selected="true">description</option> + <option value="domain_source" selected="true">domain_source</option> + <option value="full_dataset_link" selected="true">full_dataset_link</option> + <option value="id" selected="true">id</option> + <option value="instrument_platform" selected="true">instrument_platform</option> + <option value="name" selected="true">name</option> + <option value="omics_type" selected="true">omics_type</option> + <option value="publication" selected="true">publication</option> + <option value="publication_date" selected="true">publication_date</option> + <option value="study_factor" selected="true">study_factor</option> + <validator type="no_options" message="Please select at least one field" /> + </param> + <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> + <param name="query_field" type="select" label="Fields" > + <option value="CHEBI">CHEBI</option> + <option value="PUBMED">PUBMED</option> + <option value="acc">acc</option> + <option value="class_comparison">class_comparison</option> + <option value="corresponding_author_email">corresponding_author_email</option> + <option value="corresponding_author_name">corresponding_author_name</option> + <option value="corresponding_author_scopusid">corresponding_author_scopusid</option> + <option value="description">description</option> + <option value="description_synonyms">description_synonyms</option> + <option value="domain_source">domain_source</option> + <option value="full_dataset_link">full_dataset_link</option> + <option value="genotypeid">genotypeid</option> + <option value="genotypeid_systematic">genotypeid_systematic</option> + <option value="id">id</option> + <option value="instrument_platform">instrument_platform</option> + <option value="kingdom">kingdom</option> + <option value="metabolite_name">metabolite_name</option> + <option value="name">name</option> + <option value="name_synonyms">name_synonyms</option> + <option value="omics_type">omics_type</option> + <option value="organism">organism</option> + <option value="organism_part">organism_part</option> + <option value="perturbationtype_level1">perturbationtype_level1</option> + <option value="perturbationtype_level2">perturbationtype_level2</option> + <option value="perturbationtype_level3">perturbationtype_level3</option> + <option value="perturbed_gene">perturbed_gene</option> + <option value="publication">publication</option> + <option value="publication_date">publication_date</option> + <option value="pubmed_abstract">pubmed_abstract</option> + <option value="pubmed_abstract_synonyms">pubmed_abstract_synonyms</option> + <option value="pubmed_authors">pubmed_authors</option> + <option value="pubmed_title">pubmed_title</option> + <option value="pubmed_title_synonyms">pubmed_title_synonyms</option> + <option value="repository">repository</option> + <option value="study_factor">study_factor</option> + <option value="submitter">submitter</option> + <option value="submitter_affiliation">submitter_affiliation</option> + <option value="submitter_email">submitter_email</option> + <option value="treatmentid">treatmentid</option> + </param> + <conditional name="comp_operation"> + <param name="operation" type="select" label="Comparison operation" > + <option value="equal">equal</option> + <option value="not">not</option> + <option value="range">range</option> + </param> + <when value="equal"> + <param name="query_text" type="text" label="Searched term"/> + </when> + <when value="not"> + <param name="query_text" type="text" label="Searched term"/> + <param name="not_query_text" type="text" label="Limiting term"/> + </when> + <when value="range"> + <param name="min" type="text" label="From"/> + <param name="max" type="text" label="To"/> + </when> + </conditional> + </repeat> + </when> + + <when value="metabolomics_workbench"> + <param name="fields" type="select" label="Fields to extract" multiple="true"> + <option value="CHEBI" selected="true">CHEBI</option> + <option value="PUBMED" selected="true">PUBMED</option> + <option value="TAXONOMY" selected="true">TAXONOMY</option> + <option value="data_protocol" selected="true">data_protocol</option> + <option value="description" selected="true">description</option> + <option value="disease" selected="true">disease</option> + <option value="domain_source" selected="true">domain_source</option> + <option value="full_dataset_link" selected="true">full_dataset_link</option> + <option value="id" selected="true">id</option> + <option value="instrument_platform" selected="true">instrument_platform</option> + <option value="name" selected="true">name</option> + <option value="omics_type" selected="true">omics_type</option> + <option value="species" selected="true">species</option> + <option value="study_factor" selected="true">study_factor</option> + <option value="submission_date" selected="true">submission_date</option> + <option value="technology_type" selected="true">technology_type</option> + <option value="tissue" selected="true">tissue</option> + <validator type="no_options" message="Please select at least one field" /> + </param> + <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> + <param name="query_field" type="select" label="Fields" > + <option value="CHEBI">CHEBI</option> + <option value="PUBMED">PUBMED</option> + <option value="TAXONOMY">TAXONOMY</option> + <option value="acc">acc</option> + <option value="data_protocol">data_protocol</option> + <option value="data_synonyms">data_synonyms</option> + <option value="description">description</option> + <option value="description_synonyms">description_synonyms</option> + <option value="disease">disease</option> + <option value="domain_source">domain_source</option> + <option value="full_dataset_link">full_dataset_link</option> + <option value="id">id</option> + <option value="instrument_platform">instrument_platform</option> + <option value="metabolite_name">metabolite_name</option> + <option value="name">name</option> + <option value="name_synonyms">name_synonyms</option> + <option value="omics_type">omics_type</option> + <option value="pubchem_id">pubchem_id</option> + <option value="pubmed_abstract">pubmed_abstract</option> + <option value="pubmed_authors">pubmed_authors</option> + <option value="pubmed_title">pubmed_title</option> + <option value="repository">repository</option> + <option value="species">species</option> + <option value="study_factor">study_factor</option> + <option value="submission_date">submission_date</option> + <option value="submitter">submitter</option> + <option value="submitter_affiliation">submitter_affiliation</option> + <option value="submitter_mail">submitter_mail</option> + <option value="technology_type">technology_type</option> + <option value="tissue">tissue</option> + </param> + <conditional name="comp_operation"> + <param name="operation" type="select" label="Comparison operation" > + <option value="equal">equal</option> + <option value="not">not</option> + <option value="range">range</option> + </param> + <when value="equal"> + <param name="query_text" type="text" label="Searched term"/> + </when> + <when value="not"> + <param name="query_text" type="text" label="Searched term"/> + <param name="not_query_text" type="text" label="Limiting term"/> + </when> + <when value="range"> + <param name="min" type="text" label="From"/> + <param name="max" type="text" label="To"/> + </when> + </conditional> + </repeat> + </when> + + <when value="hmmer_hmm"> + <param name="fields" type="select" label="Fields to extract" multiple="true"> + <option value="content" selected="true">content</option> + <option value="domain_source" selected="true">domain_source</option> + <option value="id" selected="true">id</option> + <validator type="no_options" message="Please select at least one field" /> + </param> + <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> + <param name="query_field" type="select" label="Fields" > + <option value="domain_source">domain_source</option> + <option value="id">id</option> + </param> + <conditional name="comp_operation"> + <param name="operation" type="select" label="Comparison operation" > + <option value="equal">equal</option> + <option value="not">not</option> + <option value="range">range</option> + </param> + <when value="equal"> + <param name="query_text" type="text" label="Searched term"/> + </when> + <when value="not"> + <param name="query_text" type="text" label="Searched term"/> + <param name="not_query_text" type="text" label="Limiting term"/> + </when> + <when value="range"> + <param name="min" type="text" label="From"/> + <param name="max" type="text" label="To"/> + </when> + </conditional> + </repeat> + </when> + + <when value="hmmer_seq"> + <param name="fields" type="select" label="Fields to extract" multiple="true"> + <option value="ENSEMBL" selected="true">ENSEMBL</option> + <option value="PDB" selected="true">PDB</option> + <option value="UNIPROT" selected="true">UNIPROT</option> + <option value="content" selected="true">content</option> + <option value="domain_source" selected="true">domain_source</option> + <option value="id" selected="true">id</option> + <validator type="no_options" message="Please select at least one field" /> + </param> + <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> + <param name="query_field" type="select" label="Fields" > + <option value="ENSEMBL">ENSEMBL</option> + <option value="PDB">PDB</option> + <option value="UNIPROT">UNIPROT</option> + <option value="domain_source">domain_source</option> + <option value="id">id</option> + </param> + <conditional name="comp_operation"> + <param name="operation" type="select" label="Comparison operation" > + <option value="equal">equal</option> + <option value="not">not</option> + <option value="range">range</option> + </param> + <when value="equal"> + <param name="query_text" type="text" label="Searched term"/> + </when> + <when value="not"> + <param name="query_text" type="text" label="Searched term"/> + <param name="not_query_text" type="text" label="Limiting term"/> + </when> + <when value="range"> + <param name="min" type="text" label="From"/> + <param name="max" type="text" label="To"/> + </when> + </conditional> + </repeat> + </when> + + <when value="metagenomics_projects"> + <param name="fields" type="select" label="Fields to extract" multiple="true"> + <option value="METAGENOMICS_RUNS" selected="true">METAGENOMICS_RUNS</option> + <option value="METAGENOMICS_SAMPLES" selected="true">METAGENOMICS_SAMPLES</option> + <option value="biome_name" selected="true">biome_name</option> + <option value="description" selected="true">description</option> + <option value="domain_source" selected="true">domain_source</option> + <option value="id" selected="true">id</option> + <option value="name" selected="true">name</option> + <validator type="no_options" message="Please select at least one field" /> + </param> + <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> + <param name="query_field" type="select" label="Fields" > + <option value="METAGENOMICS_RUNS">METAGENOMICS_RUNS</option> + <option value="METAGENOMICS_SAMPLES">METAGENOMICS_SAMPLES</option> + <option value="biome">biome</option> + <option value="biome_name">biome_name</option> + <option value="centre_name">centre_name</option> + <option value="creation_date">creation_date</option> + <option value="description">description</option> + <option value="domain_source">domain_source</option> + <option value="id">id</option> + <option value="last_modification_date">last_modification_date</option> + <option value="name">name</option> + <option value="releaseDate_date">releaseDate_date</option> + </param> + <conditional name="comp_operation"> + <param name="operation" type="select" label="Comparison operation" > + <option value="equal">equal</option> + <option value="not">not</option> + <option value="range">range</option> + </param> + <when value="equal"> + <param name="query_text" type="text" label="Searched term"/> + </when> + <when value="not"> + <param name="query_text" type="text" label="Searched term"/> + <param name="not_query_text" type="text" label="Limiting term"/> + </when> + <when value="range"> + <param name="min" type="text" label="From"/> + <param name="max" type="text" label="To"/> + </when> + </conditional> + </repeat> + </when> + + <when value="metagenomics_runs"> + <param name="fields" type="select" label="Fields to extract" multiple="true"> + <option value="GO" selected="true">GO</option> + <option value="INTERPRO" selected="true">INTERPRO</option> + <option value="METAGENOMICS_PROJECTS" selected="true">METAGENOMICS_PROJECTS</option> + <option value="METAGENOMICS_SAMPLES" selected="true">METAGENOMICS_SAMPLES</option> + <option value="altitude" selected="true">altitude</option> + <option value="depth" selected="true">depth</option> + <option value="domain_source" selected="true">domain_source</option> + <option value="experiment_type" selected="true">experiment_type</option> + <option value="id" selected="true">id</option> + <option value="name" selected="true">name</option> + <option value="pH" selected="true">pH</option> + <option value="pipeline_version" selected="true">pipeline_version</option> + <option value="project_name" selected="true">project_name</option> + <option value="sample_name" selected="true">sample_name</option> + <option value="temperature" selected="true">temperature</option> + <validator type="no_options" message="Please select at least one field" /> + </param> + <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> + <param name="query_field" type="select" label="Fields" > + <option value="GO">GO</option> + <option value="INTERPRO">INTERPRO</option> + <option value="METAGENOMICS_PROJECTS">METAGENOMICS_PROJECTS</option> + <option value="METAGENOMICS_SAMPLES">METAGENOMICS_SAMPLES</option> + <option value="altitude">altitude</option> + <option value="biome">biome</option> + <option value="completion_date">completion_date</option> + <option value="creation_date">creation_date</option> + <option value="depth">depth</option> + <option value="domain_source">domain_source</option> + <option value="experiment_type">experiment_type</option> + <option value="go_term">go_term</option> + <option value="id">id</option> + <option value="interpro_entry">interpro_entry</option> + <option value="name">name</option> + <option value="organism">organism</option> + <option value="pH">pH</option> + <option value="pipeline_version">pipeline_version</option> + <option value="project_name">project_name</option> + <option value="sample_name">sample_name</option> + <option value="temperature">temperature</option> + </param> + <conditional name="comp_operation"> + <param name="operation" type="select" label="Comparison operation" > + <option value="equal">equal</option> + <option value="not">not</option> + <option value="range">range</option> + </param> + <when value="equal"> + <param name="query_text" type="text" label="Searched term"/> + </when> + <when value="not"> + <param name="query_text" type="text" label="Searched term"/> + <param name="not_query_text" type="text" label="Limiting term"/> + </when> + <when value="range"> + <param name="min" type="text" label="From"/> + <param name="max" type="text" label="To"/> + </when> + </conditional> + </repeat> + </when> + + <when value="metagenomics_samples"> + <param name="fields" type="select" label="Fields to extract" multiple="true"> + <option value="ENVO" selected="true">ENVO</option> + <option value="METAGENOMICS_PROJECTS" selected="true">METAGENOMICS_PROJECTS</option> + <option value="METAGENOMICS_RUNS" selected="true">METAGENOMICS_RUNS</option> + <option value="UBERON" selected="true">UBERON</option> + <option value="biome_name" selected="true">biome_name</option> + <option value="description" selected="true">description</option> + <option value="domain_source" selected="true">domain_source</option> + <option value="id" selected="true">id</option> + <option value="name" selected="true">name</option> + <option value="project_name" selected="true">project_name</option> + <validator type="no_options" message="Please select at least one field" /> + </param> + <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> + <param name="query_field" type="select" label="Fields" > + <option value="ENVO">ENVO</option> + <option value="METAGENOMICS_PROJECTS">METAGENOMICS_PROJECTS</option> + <option value="METAGENOMICS_RUNS">METAGENOMICS_RUNS</option> + <option value="UBERON">UBERON</option> + <option value="alias">alias</option> + <option value="altitude">altitude</option> + <option value="biome">biome</option> + <option value="biome_name">biome_name</option> + <option value="body-mass_index">body-mass_index</option> + <option value="body_product">body_product</option> + <option value="collection_date">collection_date</option> + <option value="creation_date">creation_date</option> + <option value="depth">depth</option> + <option value="description">description</option> + <option value="disease_status">disease_status</option> + <option value="domain_source">domain_source</option> + <option value="elevation">elevation</option> + <option value="experiment_type">experiment_type</option> + <option value="feature">feature</option> + <option value="id">id</option> + <option value="last_modification_date">last_modification_date</option> + <option value="latitude_end">latitude_end</option> + <option value="latitude_start">latitude_start</option> + <option value="location_name">location_name</option> + <option value="longitude_end">longitude_end</option> + <option value="longitude_start">longitude_start</option> + <option value="marine_region">marine_region</option> + <option value="material">material</option> + <option value="name">name</option> + <option value="ph">ph</option> + <option value="phenotype">phenotype</option> + <option value="project_name">project_name</option> + <option value="salinity">salinity</option> + <option value="sequencing_method">sequencing_method</option> + <option value="species">species</option> + <option value="temperature">temperature</option> + </param> + <conditional name="comp_operation"> + <param name="operation" type="select" label="Comparison operation" > + <option value="equal">equal</option> + <option value="not">not</option> + <option value="range">range</option> + </param> + <when value="equal"> + <param name="query_text" type="text" label="Searched term"/> + </when> + <when value="not"> + <param name="query_text" type="text" label="Searched term"/> + <param name="not_query_text" type="text" label="Limiting term"/> + </when> + <when value="range"> + <param name="min" type="text" label="From"/> + <param name="max" type="text" label="To"/> + </when> + </conditional> + </repeat> + </when> + + <when value="nrnl1"> + <param name="fields" type="select" label="Fields to extract" multiple="true"> + <option value="EM_PAT" selected="true">EM_PAT</option> + <option value="PATENT_NUMBER" selected="true">PATENT_NUMBER</option> + <option value="domain_source" selected="true">domain_source</option> + <option value="id" selected="true">id</option> + <validator type="no_options" message="Please select at least one field" /> + </param> + <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> + <param name="query_field" type="select" label="Fields" > + <option value="EM_PAT">EM_PAT</option> + <option value="PATENT_NUMBER">PATENT_NUMBER</option> + <option value="domain_source">domain_source</option> + <option value="earliest_publication_date">earliest_publication_date</option> + <option value="id">id</option> + <option value="master_patent_publication">master_patent_publication</option> + <option value="md5">md5</option> + </param> + <conditional name="comp_operation"> + <param name="operation" type="select" label="Comparison operation" > + <option value="equal">equal</option> + <option value="not">not</option> + <option value="range">range</option> + </param> + <when value="equal"> + <param name="query_text" type="text" label="Searched term"/> + </when> + <when value="not"> + <param name="query_text" type="text" label="Searched term"/> + <param name="not_query_text" type="text" label="Limiting term"/> + </when> + <when value="range"> + <param name="min" type="text" label="From"/> + <param name="max" type="text" label="To"/> + </when> + </conditional> + </repeat> + </when> + + <when value="nrnl2"> + <param name="fields" type="select" label="Fields to extract" multiple="true"> + <option value="EM_PAT" selected="true">EM_PAT</option> + <option value="PATENTFAMILIES" selected="true">PATENTFAMILIES</option> + <option value="PATENT_NUMBER" selected="true">PATENT_NUMBER</option> + <option value="domain_source" selected="true">domain_source</option> + <option value="id" selected="true">id</option> + <validator type="no_options" message="Please select at least one field" /> + </param> + <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> + <param name="query_field" type="select" label="Fields" > + <option value="EM_PAT">EM_PAT</option> + <option value="PATENTFAMILIES">PATENTFAMILIES</option> + <option value="PATENT_NUMBER">PATENT_NUMBER</option> + <option value="domain_source">domain_source</option> + <option value="earliest_publication_date">earliest_publication_date</option> + <option value="id">id</option> + <option value="master_patent_publication">master_patent_publication</option> + <option value="md5">md5</option> + <option value="patent_priority">patent_priority</option> + <option value="patent_priority_date">patent_priority_date</option> + </param> + <conditional name="comp_operation"> + <param name="operation" type="select" label="Comparison operation" > + <option value="equal">equal</option> + <option value="not">not</option> + <option value="range">range</option> + </param> + <when value="equal"> + <param name="query_text" type="text" label="Searched term"/> + </when> + <when value="not"> + <param name="query_text" type="text" label="Searched term"/> + <param name="not_query_text" type="text" label="Limiting term"/> + </when> + <when value="range"> + <param name="min" type="text" label="From"/> + <param name="max" type="text" label="To"/> + </when> + </conditional> + </repeat> + </when> + + <when value="nrpl1"> + <param name="fields" type="select" label="Fields to extract" multiple="true"> + <option value="EPOP" selected="true">EPOP</option> + <option value="JPOP" selected="true">JPOP</option> + <option value="KPOP" selected="true">KPOP</option> + <option value="PATENT_NUMBER" selected="true">PATENT_NUMBER</option> + <option value="USPOP" selected="true">USPOP</option> + <option value="domain_source" selected="true">domain_source</option> + <option value="id" selected="true">id</option> + <validator type="no_options" message="Please select at least one field" /> + </param> + <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> + <param name="query_field" type="select" label="Fields" > + <option value="EPOP">EPOP</option> + <option value="JPOP">JPOP</option> + <option value="KPOP">KPOP</option> + <option value="PATENT_NUMBER">PATENT_NUMBER</option> + <option value="USPOP">USPOP</option> + <option value="domain_source">domain_source</option> + <option value="earliest_publication_date">earliest_publication_date</option> + <option value="id">id</option> + <option value="master_patent_publication">master_patent_publication</option> + <option value="md5">md5</option> + </param> + <conditional name="comp_operation"> + <param name="operation" type="select" label="Comparison operation" > + <option value="equal">equal</option> + <option value="not">not</option> + <option value="range">range</option> + </param> + <when value="equal"> + <param name="query_text" type="text" label="Searched term"/> + </when> + <when value="not"> + <param name="query_text" type="text" label="Searched term"/> + <param name="not_query_text" type="text" label="Limiting term"/> + </when> + <when value="range"> + <param name="min" type="text" label="From"/> + <param name="max" type="text" label="To"/> + </when> + </conditional> + </repeat> + </when> + + <when value="nrpl2"> + <param name="fields" type="select" label="Fields to extract" multiple="true"> + <option value="EPOP" selected="true">EPOP</option> + <option value="JPOP" selected="true">JPOP</option> + <option value="KPOP" selected="true">KPOP</option> + <option value="PATENTFAMILIES" selected="true">PATENTFAMILIES</option> + <option value="PATENT_NUMBER" selected="true">PATENT_NUMBER</option> + <option value="USPOP" selected="true">USPOP</option> + <option value="domain_source" selected="true">domain_source</option> + <option value="id" selected="true">id</option> + <validator type="no_options" message="Please select at least one field" /> + </param> + <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> + <param name="query_field" type="select" label="Fields" > + <option value="EPOP">EPOP</option> + <option value="JPOP">JPOP</option> + <option value="KPOP">KPOP</option> + <option value="PATENTFAMILIES">PATENTFAMILIES</option> + <option value="PATENT_NUMBER">PATENT_NUMBER</option> + <option value="USPOP">USPOP</option> + <option value="domain_source">domain_source</option> + <option value="earliest_publication_date">earliest_publication_date</option> + <option value="id">id</option> + <option value="master_patent_publication">master_patent_publication</option> + <option value="md5">md5</option> + <option value="patent_priority">patent_priority</option> + <option value="patent_priority_date">patent_priority_date</option> + </param> + <conditional name="comp_operation"> + <param name="operation" type="select" label="Comparison operation" > + <option value="equal">equal</option> + <option value="not">not</option> + <option value="range">range</option> + </param> + <when value="equal"> + <param name="query_text" type="text" label="Searched term"/> + </when> + <when value="not"> + <param name="query_text" type="text" label="Searched term"/> + <param name="not_query_text" type="text" label="Limiting term"/> + </when> + <when value="range"> + <param name="min" type="text" label="From"/> + <param name="max" type="text" label="To"/> + </when> + </conditional> + </repeat> + </when> + + <when value="non-coding_release"> + <param name="fields" type="select" label="Fields to extract" multiple="true"> + <option value="AGRICOLA" selected="true">AGRICOLA</option> + <option value="BIOSAMPLE" selected="true">BIOSAMPLE</option> + <option value="DOI" selected="true">DOI</option> + <option value="EMBL" selected="true">EMBL</option> + <option value="GTRNADB" selected="true">GTRNADB</option> + <option value="LNCRNADB" selected="true">LNCRNADB</option> + <option value="MIRBASE" selected="true">MIRBASE</option> + <option value="PATENT_NUMBER" selected="true">PATENT_NUMBER</option> + <option value="POMBASE" selected="true">POMBASE</option> + <option value="PUBMED" selected="true">PUBMED</option> + <option value="SILVA-LSU" selected="true">SILVA-LSU</option> + <option value="SILVA-SSU" selected="true">SILVA-SSU</option> + <option value="SRPDB" selected="true">SRPDB</option> + <option value="TAXON" selected="true">TAXON</option> + <option value="TMRNA-WEBSITE" selected="true">TMRNA-WEBSITE</option> + <option value="UNILIB" selected="true">UNILIB</option> + <option value="VEGA-GN" selected="true">VEGA-GN</option> + <option value="VEGA-TR" selected="true">VEGA-TR</option> + <option value="WORMBASE" selected="true">WORMBASE</option> + <option value="description" selected="true">description</option> + <option value="domain_source" selected="true">domain_source</option> + <option value="id" selected="true">id</option> + <validator type="no_options" message="Please select at least one field" /> + </param> + <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> + <param name="query_field" type="select" label="Fields" > + <option value="AGRICOLA">AGRICOLA</option> + <option value="BIOSAMPLE">BIOSAMPLE</option> + <option value="DOI">DOI</option> + <option value="EMBL">EMBL</option> + <option value="GTRNADB">GTRNADB</option> + <option value="LNCRNADB">LNCRNADB</option> + <option value="MD5">MD5</option> + <option value="MIRBASE">MIRBASE</option> + <option value="PATENT_NUMBER">PATENT_NUMBER</option> + <option value="POMBASE">POMBASE</option> + <option value="PROJECT">PROJECT</option> + <option value="PUBMED">PUBMED</option> + <option value="SILVA-LSU">SILVA-LSU</option> + <option value="SILVA-SSU">SILVA-SSU</option> + <option value="SRPDB">SRPDB</option> + <option value="TAXON">TAXON</option> + <option value="TMRNA-WEBSITE">TMRNA-WEBSITE</option> + <option value="UNILIB">UNILIB</option> + <option value="VEGA-GN">VEGA-GN</option> + <option value="VEGA-TR">VEGA-TR</option> + <option value="WORMBASE">WORMBASE</option> + <option value="bio_material">bio_material</option> + <option value="creation_date">creation_date</option> + <option value="culture_collection">culture_collection</option> + <option value="data_class">data_class</option> + <option value="description">description</option> + <option value="division">division</option> + <option value="domain_source">domain_source</option> + <option value="gene">gene</option> + <option value="gene_synonym">gene_synonym</option> + <option value="id">id</option> + <option value="keywords">keywords</option> + <option value="last_modification_date">last_modification_date</option> + <option value="length">length</option> + <option value="locus_tag">locus_tag</option> + <option value="molecule_type">molecule_type</option> + <option value="old_locus_tag">old_locus_tag</option> + <option value="organelle">organelle</option> + <option value="organism">organism</option> + <option value="organism_classification">organism_classification</option> + <option value="organism_species">organism_species</option> + <option value="product">product</option> + <option value="references">references</option> + <option value="sequence_version">sequence_version</option> + <option value="specimen_voucher">specimen_voucher</option> + <option value="topology">topology</option> + </param> + <conditional name="comp_operation"> + <param name="operation" type="select" label="Comparison operation" > + <option value="equal">equal</option> + <option value="not">not</option> + <option value="range">range</option> + </param> + <when value="equal"> + <param name="query_text" type="text" label="Searched term"/> + </when> + <when value="not"> + <param name="query_text" type="text" label="Searched term"/> + <param name="not_query_text" type="text" label="Limiting term"/> + </when> + <when value="range"> + <param name="min" type="text" label="From"/> + <param name="max" type="text" label="To"/> + </when> + </conditional> + </repeat> + </when> + + <when value="non-coding_update"> + <param name="fields" type="select" label="Fields to extract" multiple="true"> + <option value="AGRICOLA" selected="true">AGRICOLA</option> + <option value="BIOSAMPLE" selected="true">BIOSAMPLE</option> + <option value="DOI" selected="true">DOI</option> + <option value="EMBL" selected="true">EMBL</option> + <option value="PATENT_NUMBER" selected="true">PATENT_NUMBER</option> + <option value="PUBMED" selected="true">PUBMED</option> + <option value="SILVA-LSU" selected="true">SILVA-LSU</option> + <option value="SILVA-SSU" selected="true">SILVA-SSU</option> + <option value="TAXON" selected="true">TAXON</option> + <option value="WORMBASE" selected="true">WORMBASE</option> + <option value="description" selected="true">description</option> + <option value="domain_source" selected="true">domain_source</option> + <option value="id" selected="true">id</option> + <validator type="no_options" message="Please select at least one field" /> + </param> + <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> + <param name="query_field" type="select" label="Fields" > + <option value="AGRICOLA">AGRICOLA</option> + <option value="BIOSAMPLE">BIOSAMPLE</option> + <option value="DOI">DOI</option> + <option value="EMBL">EMBL</option> + <option value="MD5">MD5</option> + <option value="PATENT_NUMBER">PATENT_NUMBER</option> + <option value="PROJECT">PROJECT</option> + <option value="PUBMED">PUBMED</option> + <option value="SILVA-LSU">SILVA-LSU</option> + <option value="SILVA-SSU">SILVA-SSU</option> + <option value="TAXON">TAXON</option> + <option value="WORMBASE">WORMBASE</option> + <option value="bio_material">bio_material</option> + <option value="creation_date">creation_date</option> + <option value="culture_collection">culture_collection</option> + <option value="data_class">data_class</option> + <option value="description">description</option> + <option value="division">division</option> + <option value="domain_source">domain_source</option> + <option value="gene">gene</option> + <option value="gene_synonym">gene_synonym</option> + <option value="id">id</option> + <option value="keywords">keywords</option> + <option value="last_modification_date">last_modification_date</option> + <option value="length">length</option> + <option value="locus_tag">locus_tag</option> + <option value="molecule_type">molecule_type</option> + <option value="old_locus_tag">old_locus_tag</option> + <option value="organelle">organelle</option> + <option value="organism">organism</option> + <option value="organism_classification">organism_classification</option> + <option value="organism_species">organism_species</option> + <option value="product">product</option> + <option value="references">references</option> + <option value="sequence_version">sequence_version</option> + <option value="specimen_voucher">specimen_voucher</option> + <option value="topology">topology</option> + </param> + <conditional name="comp_operation"> + <param name="operation" type="select" label="Comparison operation" > + <option value="equal">equal</option> + <option value="not">not</option> + <option value="range">range</option> + </param> + <when value="equal"> + <param name="query_text" type="text" label="Searched term"/> + </when> + <when value="not"> + <param name="query_text" type="text" label="Searched term"/> + <param name="not_query_text" type="text" label="Limiting term"/> + </when> + <when value="range"> + <param name="min" type="text" label="From"/> + <param name="max" type="text" label="To"/> + </when> + </conditional> + </repeat> + </when> + + <when value="omim"> + <param name="fields" type="select" label="Fields to extract" multiple="true"> + <option value="OMIM" selected="true">OMIM</option> + <option value="description" selected="true">description</option> + <option value="domain_source" selected="true">domain_source</option> + <option value="id" selected="true">id</option> + <option value="title" selected="true">title</option> + <validator type="no_options" message="Please select at least one field" /> + </param> + <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> + <param name="query_field" type="select" label="Fields" > + <option value="OMIM">OMIM</option> + <option value="allelic_variations">allelic_variations</option> + <option value="alternative_title">alternative_title</option> + <option value="clinical_synopsis">clinical_synopsis</option> + <option value="creation_date">creation_date</option> + <option value="description">description</option> + <option value="domain_source">domain_source</option> + <option value="id">id</option> + <option value="references">references</option> + <option value="see_also">see_also</option> + <option value="title">title</option> + </param> + <conditional name="comp_operation"> + <param name="operation" type="select" label="Comparison operation" > + <option value="equal">equal</option> + <option value="not">not</option> + <option value="range">range</option> + </param> + <when value="equal"> + <param name="query_text" type="text" label="Searched term"/> + </when> + <when value="not"> + <param name="query_text" type="text" label="Searched term"/> + <param name="not_query_text" type="text" label="Limiting term"/> + </when> + <when value="range"> + <param name="min" type="text" label="From"/> + <param name="max" type="text" label="To"/> + </when> + </conditional> + </repeat> + </when> + + <when value="pdbe"> + <param name="fields" type="select" label="Fields to extract" multiple="true"> + <option value="CATH" selected="true">CATH</option> + <option value="EC" selected="true">EC</option> + <option value="GO" selected="true">GO</option> + <option value="INTERPRO" selected="true">INTERPRO</option> + <option value="MSDSD" selected="true">MSDSD</option> + <option value="PFAM" selected="true">PFAM</option> + <option value="PUBMED" selected="true">PUBMED</option> + <option value="SCOP" selected="true">SCOP</option> + <option value="TAXONOMY" selected="true">TAXONOMY</option> + <option value="UNIPROT" selected="true">UNIPROT</option> + <option value="acc" selected="true">acc</option> + <option value="description" selected="true">description</option> + <option value="domain_source" selected="true">domain_source</option> + <option value="id" selected="true">id</option> + <option value="name" selected="true">name</option> + <validator type="no_options" message="Please select at least one field" /> + </param> + <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> + <param name="query_field" type="select" label="Fields" > + <option value="CATH">CATH</option> + <option value="EC">EC</option> + <option value="GO">GO</option> + <option value="INTERPRO">INTERPRO</option> + <option value="MSDSD">MSDSD</option> + <option value="PFAM">PFAM</option> + <option value="PUBMED">PUBMED</option> + <option value="SCOP">SCOP</option> + <option value="TAXONOMY">TAXONOMY</option> + <option value="UNIPROT">UNIPROT</option> + <option value="acc">acc</option> + <option value="assembly">assembly</option> + <option value="author">author</option> + <option value="chain">chain</option> + <option value="citation">citation</option> + <option value="creation_date">creation_date</option> + <option value="description">description</option> + <option value="domain_source">domain_source</option> + <option value="experiment_type">experiment_type</option> + <option value="id">id</option> + <option value="keywords">keywords</option> + <option value="last_modification_date">last_modification_date</option> + <option value="ligand">ligand</option> + <option value="name">name</option> + <option value="resolution">resolution</option> + <option value="source_organism">source_organism</option> + </param> + <conditional name="comp_operation"> + <param name="operation" type="select" label="Comparison operation" > + <option value="equal">equal</option> + <option value="not">not</option> + <option value="range">range</option> + </param> + <when value="equal"> + <param name="query_text" type="text" label="Searched term"/> + </when> + <when value="not"> + <param name="query_text" type="text" label="Searched term"/> + <param name="not_query_text" type="text" label="Limiting term"/> + </when> + <when value="range"> + <param name="min" type="text" label="From"/> + <param name="max" type="text" label="To"/> + </when> + </conditional> + </repeat> + </when> + + <when value="pride"> + <param name="fields" type="select" label="Fields to extract" multiple="true"> + <option value="ENSEMBL" selected="true">ENSEMBL</option> + <option value="PUBMED" selected="true">PUBMED</option> + <option value="TAXONOMY" selected="true">TAXONOMY</option> + <option value="UNIPROT" selected="true">UNIPROT</option> + <option value="data_protocol" selected="true">data_protocol</option> + <option value="dataset_file" selected="true">dataset_file</option> + <option value="description" selected="true">description</option> + <option value="disease" selected="true">disease</option> + <option value="domain_source" selected="true">domain_source</option> + <option value="full_dataset_link" selected="true">full_dataset_link</option> + <option value="id" selected="true">id</option> + <option value="instrument_platform" selected="true">instrument_platform</option> + <option value="labhead" selected="true">labhead</option> + <option value="labhead_affiliation" selected="true">labhead_affiliation</option> + <option value="labhead_mail" selected="true">labhead_mail</option> + <option value="modification" selected="true">modification</option> + <option value="name" selected="true">name</option> + <option value="omics_type" selected="true">omics_type</option> + <option value="publication" selected="true">publication</option> + <option value="publication_date" selected="true">publication_date</option> + <option value="sample_protocol" selected="true">sample_protocol</option> + <option value="species" selected="true">species</option> + <option value="submission_date" selected="true">submission_date</option> + <option value="submitter_keywords" selected="true">submitter_keywords</option> + <option value="technology_type" selected="true">technology_type</option> + <option value="tissue" selected="true">tissue</option> + <validator type="no_options" message="Please select at least one field" /> + </param> + <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> + <param name="query_field" type="select" label="Fields" > + <option value="ENSEMBL">ENSEMBL</option> + <option value="PUBMED">PUBMED</option> + <option value="TAXONOMY">TAXONOMY</option> + <option value="UNIPROT">UNIPROT</option> + <option value="acc">acc</option> + <option value="cell_type">cell_type</option> + <option value="curator_keywords">curator_keywords</option> + <option value="data_protocol">data_protocol</option> + <option value="data_synonyms">data_synonyms</option> + <option value="description">description</option> + <option value="description_synonyms">description_synonyms</option> + <option value="disease">disease</option> + <option value="doi">doi</option> + <option value="domain_source">domain_source</option> + <option value="full_dataset_link">full_dataset_link</option> + <option value="id">id</option> + <option value="instrument_platform">instrument_platform</option> + <option value="labhead">labhead</option> + <option value="labhead_affiliation">labhead_affiliation</option> + <option value="labhead_mail">labhead_mail</option> + <option value="modification">modification</option> + <option value="name">name</option> + <option value="name_synonyms">name_synonyms</option> + <option value="omics_type">omics_type</option> + <option value="publication">publication</option> + <option value="publication_date">publication_date</option> + <option value="pubmed_abstract">pubmed_abstract</option> + <option value="pubmed_abstract_synonyms">pubmed_abstract_synonyms</option> + <option value="pubmed_authors">pubmed_authors</option> + <option value="pubmed_title">pubmed_title</option> + <option value="pubmed_title_synonyms">pubmed_title_synonyms</option> + <option value="quantification_method">quantification_method</option> + <option value="repository">repository</option> + <option value="sample_protocol">sample_protocol</option> + <option value="sample_synonyms">sample_synonyms</option> + <option value="software">software</option> + <option value="species">species</option> + <option value="submission_date">submission_date</option> + <option value="submission_type">submission_type</option> + <option value="submitter">submitter</option> + <option value="submitter_affiliation">submitter_affiliation</option> + <option value="submitter_keywords">submitter_keywords</option> + <option value="submitter_mail">submitter_mail</option> + <option value="technology_type">technology_type</option> + <option value="tissue">tissue</option> + </param> + <conditional name="comp_operation"> + <param name="operation" type="select" label="Comparison operation" > + <option value="equal">equal</option> + <option value="not">not</option> + <option value="range">range</option> + </param> + <when value="equal"> + <param name="query_text" type="text" label="Searched term"/> + </when> + <when value="not"> + <param name="query_text" type="text" label="Searched term"/> + <param name="not_query_text" type="text" label="Limiting term"/> + </when> + <when value="range"> + <param name="min" type="text" label="From"/> + <param name="max" type="text" label="To"/> + </when> + </conditional> + </repeat> + </when> + + <when value="patentFamilies"> + <param name="fields" type="select" label="Fields to extract" multiple="true"> + <option value="PATENT_NUMBER" selected="true">PATENT_NUMBER</option> + <option value="domain_source" selected="true">domain_source</option> + <option value="id" selected="true">id</option> + <validator type="no_options" message="Please select at least one field" /> + </param> + <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> + <param name="query_field" type="select" label="Fields" > + <option value="PATENT_NUMBER">PATENT_NUMBER</option> + <option value="domain_source">domain_source</option> + <option value="id">id</option> + <option value="master_patent_publication">master_patent_publication</option> + <option value="patent_priority">patent_priority</option> + </param> + <conditional name="comp_operation"> + <param name="operation" type="select" label="Comparison operation" > + <option value="equal">equal</option> + <option value="not">not</option> + <option value="range">range</option> + </param> + <when value="equal"> + <param name="query_text" type="text" label="Searched term"/> + </when> + <when value="not"> + <param name="query_text" type="text" label="Searched term"/> + <param name="not_query_text" type="text" label="Limiting term"/> + </when> + <when value="range"> + <param name="min" type="text" label="From"/> + <param name="max" type="text" label="To"/> + </when> + </conditional> + </repeat> + </when> + + <when value="patentdb"> + <param name="fields" type="select" label="Fields to extract" multiple="true"> + <option value="EPO" selected="true">EPO</option> + <option value="IPC" selected="true">IPC</option> + <option value="description" selected="true">description</option> + <option value="domain_source" selected="true">domain_source</option> + <option value="id" selected="true">id</option> + <option value="name" selected="true">name</option> + <option value="patent_number" selected="true">patent_number</option> + <option value="publication_date" selected="true">publication_date</option> + <validator type="no_options" message="Please select at least one field" /> + </param> + <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> + <param name="query_field" type="select" label="Fields" > + <option value="EPO">EPO</option> + <option value="IPC">IPC</option> + <option value="MC">MC</option> + <option value="application_date">application_date</option> + <option value="author">author</option> + <option value="datasource">datasource</option> + <option value="description">description</option> + <option value="designated_states">designated_states</option> + <option value="domain_source">domain_source</option> + <option value="id">id</option> + <option value="name">name</option> + <option value="patent_number">patent_number</option> + <option value="publication_date">publication_date</option> + <option value="type">type</option> + </param> + <conditional name="comp_operation"> + <param name="operation" type="select" label="Comparison operation" > + <option value="equal">equal</option> + <option value="not">not</option> + <option value="range">range</option> + </param> + <when value="equal"> + <param name="query_text" type="text" label="Searched term"/> + </when> + <when value="not"> + <param name="query_text" type="text" label="Searched term"/> + <param name="not_query_text" type="text" label="Limiting term"/> + </when> + <when value="range"> + <param name="min" type="text" label="From"/> + <param name="max" type="text" label="To"/> + </when> + </conditional> + </repeat> + </when> + + <when value="ebiweb_people"> + <param name="fields" type="select" label="Fields to extract" multiple="true"> + <option value="domain_source" selected="true">domain_source</option> + <option value="email" selected="true">email</option> + <option value="fax" selected="true">fax</option> + <option value="forename" selected="true">forename</option> + <option value="group" selected="true">group</option> + <option value="id" selected="true">id</option> + <option value="image" selected="true">image</option> + <option value="keyname" selected="true">keyname</option> + <option value="position" selected="true">position</option> + <option value="room" selected="true">room</option> + <option value="surname" selected="true">surname</option> + <option value="tel" selected="true">tel</option> + <validator type="no_options" message="Please select at least one field" /> + </param> + <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> + <param name="query_field" type="select" label="Fields" > + <option value="bio">bio</option> + <option value="domain_source">domain_source</option> + <option value="email">email</option> + <option value="fax">fax</option> + <option value="forename">forename</option> + <option value="group">group</option> + <option value="id">id</option> + <option value="resource">resource</option> + <option value="role">role</option> + <option value="room">room</option> + <option value="surname">surname</option> + <option value="tel">tel</option> + </param> + <conditional name="comp_operation"> + <param name="operation" type="select" label="Comparison operation" > + <option value="equal">equal</option> + <option value="not">not</option> + <option value="range">range</option> + </param> + <when value="equal"> + <param name="query_text" type="text" label="Searched term"/> + </when> + <when value="not"> + <param name="query_text" type="text" label="Searched term"/> + <param name="not_query_text" type="text" label="Limiting term"/> + </when> + <when value="range"> + <param name="min" type="text" label="From"/> + <param name="max" type="text" label="To"/> + </when> + </conditional> + </repeat> + </when> + + <when value="peptide_atlas"> + <param name="fields" type="select" label="Fields to extract" multiple="true"> + <option value="ENSEMBL" selected="true">ENSEMBL</option> + <option value="FLYBASE" selected="true">FLYBASE</option> + <option value="INSECTBASE" selected="true">INSECTBASE</option> + <option value="IPI" selected="true">IPI</option> + <option value="NCBI" selected="true">NCBI</option> + <option value="PASS" selected="true">PASS</option> + <option value="PRIDE" selected="true">PRIDE</option> + <option value="PUBMED" selected="true">PUBMED</option> + <option value="SGD" selected="true">SGD</option> + <option value="TAXONOMY" selected="true">TAXONOMY</option> + <option value="UNIPROT" selected="true">UNIPROT</option> + <option value="UNKNOWN" selected="true">UNKNOWN</option> + <option value="WORMGENE" selected="true">WORMGENE</option> + <option value="description" selected="true">description</option> + <option value="disease" selected="true">disease</option> + <option value="domain_source" selected="true">domain_source</option> + <option value="full_dataset_link" selected="true">full_dataset_link</option> + <option value="id" selected="true">id</option> + <option value="instrument_platform" selected="true">instrument_platform</option> + <option value="labhead" selected="true">labhead</option> + <option value="labhead_affiliation" selected="true">labhead_affiliation</option> + <option value="labhead_mail" selected="true">labhead_mail</option> + <option value="modification" selected="true">modification</option> + <option value="name" selected="true">name</option> + <option value="omics_type" selected="true">omics_type</option> + <option value="publication" selected="true">publication</option> + <option value="publication_date" selected="true">publication_date</option> + <option value="species" selected="true">species</option> + <option value="technology_type" selected="true">technology_type</option> + <option value="tissue" selected="true">tissue</option> + <validator type="no_options" message="Please select at least one field" /> + </param> + <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> + <param name="query_field" type="select" label="Fields" > + <option value="ENSEMBL">ENSEMBL</option> + <option value="FLYBASE">FLYBASE</option> + <option value="INSECTBASE">INSECTBASE</option> + <option value="IPI">IPI</option> + <option value="NCBI">NCBI</option> + <option value="PASS">PASS</option> + <option value="PRIDE">PRIDE</option> + <option value="PUBMED">PUBMED</option> + <option value="SGD">SGD</option> + <option value="TAXONOMY">TAXONOMY</option> + <option value="UNIPROT">UNIPROT</option> + <option value="UNKNOWN">UNKNOWN</option> + <option value="WORMGENE">WORMGENE</option> + <option value="acc">acc</option> + <option value="cell_type">cell_type</option> + <option value="curator_keywords">curator_keywords</option> + <option value="description">description</option> + <option value="description_synonyms">description_synonyms</option> + <option value="disease">disease</option> + <option value="domain_source">domain_source</option> + <option value="export_date">export_date</option> + <option value="full_dataset_link">full_dataset_link</option> + <option value="id">id</option> + <option value="instrument_platform">instrument_platform</option> + <option value="labhead">labhead</option> + <option value="labhead_affiliation">labhead_affiliation</option> + <option value="labhead_mail">labhead_mail</option> + <option value="modification">modification</option> + <option value="name">name</option> + <option value="name_synonyms">name_synonyms</option> + <option value="omics_type">omics_type</option> + <option value="publication">publication</option> + <option value="publication_date">publication_date</option> + <option value="pubmed_abstract">pubmed_abstract</option> + <option value="pubmed_abstract_synonyms">pubmed_abstract_synonyms</option> + <option value="pubmed_authors">pubmed_authors</option> + <option value="pubmed_title">pubmed_title</option> + <option value="pubmed_title_synonyms">pubmed_title_synonyms</option> + <option value="quantification_method">quantification_method</option> + <option value="repository">repository</option> + <option value="software">software</option> + <option value="species">species</option> + <option value="submitter">submitter</option> + <option value="submitter_affiliation">submitter_affiliation</option> + <option value="submitter_email">submitter_email</option> + <option value="submitter_mail">submitter_mail</option> + <option value="technology_type">technology_type</option> + <option value="tissue">tissue</option> + </param> + <conditional name="comp_operation"> + <param name="operation" type="select" label="Comparison operation" > + <option value="equal">equal</option> + <option value="not">not</option> + <option value="range">range</option> + </param> + <when value="equal"> + <param name="query_text" type="text" label="Searched term"/> + </when> + <when value="not"> + <param name="query_text" type="text" label="Searched term"/> + <param name="not_query_text" type="text" label="Limiting term"/> + </when> + <when value="range"> + <param name="min" type="text" label="From"/> + <param name="max" type="text" label="To"/> + </when> + </conditional> + </repeat> + </when> + + <when value="pfam"> + <param name="fields" type="select" label="Fields to extract" multiple="true"> + <option value="GO" selected="true">GO</option> + <option value="INTERPRO" selected="true">INTERPRO</option> + <option value="acc" selected="true">acc</option> + <option value="description" selected="true">description</option> + <option value="domain_source" selected="true">domain_source</option> + <option value="id" selected="true">id</option> + <option value="name" selected="true">name</option> + <option value="type" selected="true">type</option> + <validator type="no_options" message="Please select at least one field" /> + </param> + <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> + <param name="query_field" type="select" label="Fields" > + <option value="GO">GO</option> + <option value="INTERPRO">INTERPRO</option> + <option value="acc">acc</option> + <option value="author">author</option> + <option value="comment">comment</option> + <option value="component">component</option> + <option value="creation_date">creation_date</option> + <option value="description">description</option> + <option value="domain_source">domain_source</option> + <option value="function">function</option> + <option value="id">id</option> + <option value="interproabstract">interproabstract</option> + <option value="last_modified_date">last_modified_date</option> + <option value="name">name</option> + <option value="process">process</option> + <option value="type">type</option> + </param> + <conditional name="comp_operation"> + <param name="operation" type="select" label="Comparison operation" > + <option value="equal">equal</option> + <option value="not">not</option> + <option value="range">range</option> + </param> + <when value="equal"> + <param name="query_text" type="text" label="Searched term"/> + </when> + <when value="not"> + <param name="query_text" type="text" label="Searched term"/> + <param name="not_query_text" type="text" label="Limiting term"/> + </when> + <when value="range"> + <param name="min" type="text" label="From"/> + <param name="max" type="text" label="To"/> + </when> + </conditional> + </repeat> + </when> + + <when value="pombase"> + <param name="fields" type="select" label="Fields to extract" multiple="true"> + <option value="EC_NUMBER" selected="true">EC_NUMBER</option> + <option value="EMBL" selected="true">EMBL</option> + <option value="ENTREZGENE" selected="true">ENTREZGENE</option> + <option value="GO" selected="true">GO</option> + <option value="INTERPRO" selected="true">INTERPRO</option> + <option value="KEGG" selected="true">KEGG</option> + <option value="KEGG_ENZYME" selected="true">KEGG_ENZYME</option> + <option value="METACYC" selected="true">METACYC</option> + <option value="NCBI_TAXONOMY_ID" selected="true">NCBI_TAXONOMY_ID</option> + <option value="PDB" selected="true">PDB</option> + <option value="PROTEIN_ID" selected="true">PROTEIN_ID</option> + <option value="PUBMED" selected="true">PUBMED</option> + <option value="REFSEQ_MRNA" selected="true">REFSEQ_MRNA</option> + <option value="REFSEQ_MRNA_PREDICTED" selected="true">REFSEQ_MRNA_PREDICTED</option> + <option value="REFSEQ_PEPTIDE" selected="true">REFSEQ_PEPTIDE</option> + <option value="REFSEQ_PEPTIDE_PREDICTED" selected="true">REFSEQ_PEPTIDE_PREDICTED</option> + <option value="RFAM" selected="true">RFAM</option> + <option value="SO" selected="true">SO</option> + <option value="SPD" selected="true">SPD</option> + <option value="UNIPARC" selected="true">UNIPARC</option> + <option value="UNIPROT" selected="true">UNIPROT</option> + <option value="WIKIGENE" selected="true">WIKIGENE</option> + <option value="description" selected="true">description</option> + <option value="domain_source" selected="true">domain_source</option> + <option value="exon" selected="true">exon</option> + <option value="exon_count" selected="true">exon_count</option> + <option value="featuretype" selected="true">featuretype</option> + <option value="gene_name" selected="true">gene_name</option> + <option value="gene_synonym" selected="true">gene_synonym</option> + <option value="id" selected="true">id</option> + <option value="name" selected="true">name</option> + <option value="peptide" selected="true">peptide</option> + <option value="source" selected="true">source</option> + <option value="species" selected="true">species</option> + <option value="system_name" selected="true">system_name</option> + <option value="transcript" selected="true">transcript</option> + <option value="transcript_count" selected="true">transcript_count</option> + <validator type="no_options" message="Please select at least one field" /> + </param> + <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> + <param name="query_field" type="select" label="Fields" > + <option value="EC_NUMBER">EC_NUMBER</option> + <option value="EMBL">EMBL</option> + <option value="ENSEMBLVARIATION">ENSEMBLVARIATION</option> + <option value="ENTREZGENE">ENTREZGENE</option> + <option value="FYPO">FYPO</option> + <option value="GO">GO</option> + <option value="INTERPRO">INTERPRO</option> + <option value="KEGG">KEGG</option> + <option value="KEGG_ENZYME">KEGG_ENZYME</option> + <option value="METACYC">METACYC</option> + <option value="MOD">MOD</option> + <option value="NCBI_TAXONOMY_ID">NCBI_TAXONOMY_ID</option> + <option value="PBO">PBO</option> + <option value="PDB">PDB</option> + <option value="POMBASE_GENE_NAME">POMBASE_GENE_NAME</option> + <option value="POMBASE_ORTHOLOG">POMBASE_ORTHOLOG</option> + <option value="POMBASE_TRANSCRIPT">POMBASE_TRANSCRIPT</option> + <option value="POMBASE_TRANSLATION">POMBASE_TRANSLATION</option> + <option value="PROTEIN_ID">PROTEIN_ID</option> + <option value="PUBMED">PUBMED</option> + <option value="PUBMED_POMBASE">PUBMED_POMBASE</option> + <option value="REFSEQ_MRNA">REFSEQ_MRNA</option> + <option value="REFSEQ_MRNA_PREDICTED">REFSEQ_MRNA_PREDICTED</option> + <option value="REFSEQ_PEPTIDE">REFSEQ_PEPTIDE</option> + <option value="REFSEQ_PEPTIDE_PREDICTED">REFSEQ_PEPTIDE_PREDICTED</option> + <option value="RFAM">RFAM</option> + <option value="SO">SO</option> + <option value="SPD">SPD</option> + <option value="UNIPARC">UNIPARC</option> + <option value="UNIPROT">UNIPROT</option> + <option value="WIKIGENE">WIKIGENE</option> + <option value="database">database</option> + <option value="description">description</option> + <option value="domain">domain</option> + <option value="domain_count">domain_count</option> + <option value="domain_source">domain_source</option> + <option value="exon">exon</option> + <option value="gene_name">gene_name</option> + <option value="gene_synonym">gene_synonym</option> + <option value="genetree">genetree</option> + <option value="genomic_unit">genomic_unit</option> + <option value="haplotype">haplotype</option> + <option value="id">id</option> + <option value="id_noversion">id_noversion</option> + <option value="location">location</option> + <option value="name">name</option> + <option value="peptide">peptide</option> + <option value="seq_region_name">seq_region_name</option> + <option value="source">source</option> + <option value="species">species</option> + <option value="system_name">system_name</option> + <option value="transcript">transcript</option> + </param> + <conditional name="comp_operation"> + <param name="operation" type="select" label="Comparison operation" > + <option value="equal">equal</option> + <option value="not">not</option> + <option value="range">range</option> + </param> + <when value="equal"> + <param name="query_text" type="text" label="Searched term"/> + </when> + <when value="not"> + <param name="query_text" type="text" label="Searched term"/> + <param name="not_query_text" type="text" label="Limiting term"/> + </when> + <when value="range"> + <param name="min" type="text" label="From"/> + <param name="max" type="text" label="To"/> + </when> + </conditional> + </repeat> + </when> + + <when value="rnacentral"> + <param name="fields" type="select" label="Fields to extract" multiple="true"> + <option value="DICTYBASE" selected="true">DICTYBASE</option> + <option value="DOI" selected="true">DOI</option> + <option value="ECO" selected="true">ECO</option> + <option value="ENA" selected="true">ENA</option> + <option value="GO" selected="true">GO</option> + <option value="GREENGENES" selected="true">GREENGENES</option> + <option value="GTRNADB" selected="true">GTRNADB</option> + <option value="LNCIPEDIA" selected="true">LNCIPEDIA</option> + <option value="LNCRNADB" selected="true">LNCRNADB</option> + <option value="MIRBASE" selected="true">MIRBASE</option> + <option value="MODOMICS" selected="true">MODOMICS</option> + <option value="NCBI_TAXONOMY_ID" selected="true">NCBI_TAXONOMY_ID</option> + <option value="NONCODE" selected="true">NONCODE</option> + <option value="PDBE" selected="true">PDBE</option> + <option value="POMBASE" selected="true">POMBASE</option> + <option value="PUBMED" selected="true">PUBMED</option> + <option value="RDP" selected="true">RDP</option> + <option value="REFSEQ" selected="true">REFSEQ</option> + <option value="RFAM" selected="true">RFAM</option> + <option value="SGD" selected="true">SGD</option> + <option value="SILVA" selected="true">SILVA</option> + <option value="SNOPY" selected="true">SNOPY</option> + <option value="SO" selected="true">SO</option> + <option value="SRPDB" selected="true">SRPDB</option> + <option value="TAIR" selected="true">TAIR</option> + <option value="TMRNA_WEBSITE" selected="true">TMRNA_WEBSITE</option> + <option value="VEGA" selected="true">VEGA</option> + <option value="WORMBASE" selected="true">WORMBASE</option> + <option value="active" selected="true">active</option> + <option value="boost" selected="true">boost</option> + <option value="common_name" selected="true">common_name</option> + <option value="description" selected="true">description</option> + <option value="domain_source" selected="true">domain_source</option> + <option value="expert_db" selected="true">expert_db</option> + <option value="gene" selected="true">gene</option> + <option value="gene_synonym" selected="true">gene_synonym</option> + <option value="has_genomic_coordinates" selected="true">has_genomic_coordinates</option> + <option value="id" selected="true">id</option> + <option value="length" selected="true">length</option> + <option value="n_citations" selected="true">n_citations</option> + <option value="n_xrefs" selected="true">n_xrefs</option> + <option value="name" selected="true">name</option> + <option value="organelle" selected="true">organelle</option> + <option value="product" selected="true">product</option> + <option value="pub_title" selected="true">pub_title</option> + <option value="rna_type" selected="true">rna_type</option> + <option value="species" selected="true">species</option> + <validator type="no_options" message="Please select at least one field" /> + </param> + <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> + <param name="query_field" type="select" label="Fields" > + <option value="DICTYBASE">DICTYBASE</option> + <option value="DOI">DOI</option> + <option value="ECO">ECO</option> + <option value="ENA">ENA</option> + <option value="GO">GO</option> + <option value="GREENGENES">GREENGENES</option> + <option value="GTRNADB">GTRNADB</option> + <option value="LNCIPEDIA">LNCIPEDIA</option> + <option value="LNCRNADB">LNCRNADB</option> + <option value="MIRBASE">MIRBASE</option> + <option value="MODOMICS">MODOMICS</option> + <option value="NCBI_TAXONOMY_ID">NCBI_TAXONOMY_ID</option> + <option value="NONCODE">NONCODE</option> + <option value="PDBE">PDBE</option> + <option value="POMBASE">POMBASE</option> + <option value="PUBMED">PUBMED</option> + <option value="RDP">RDP</option> + <option value="REFSEQ">REFSEQ</option> + <option value="RFAM">RFAM</option> + <option value="SGD">SGD</option> + <option value="SILVA">SILVA</option> + <option value="SNOPY">SNOPY</option> + <option value="SO">SO</option> + <option value="SRPDB">SRPDB</option> + <option value="TAIR">TAIR</option> + <option value="TMRNA_WEBSITE">TMRNA_WEBSITE</option> + <option value="VEGA">VEGA</option> + <option value="WORMBASE">WORMBASE</option> + <option value="active">active</option> + <option value="author">author</option> + <option value="boost">boost</option> + <option value="common_name">common_name</option> + <option value="description">description</option> + <option value="domain_source">domain_source</option> + <option value="expert_db">expert_db</option> + <option value="first_seen_date">first_seen_date</option> + <option value="function">function</option> + <option value="gene">gene</option> + <option value="gene_synonym">gene_synonym</option> + <option value="has_genomic_coordinates">has_genomic_coordinates</option> + <option value="id">id</option> + <option value="insdc_submission">insdc_submission</option> + <option value="journal">journal</option> + <option value="last_seen_date">last_seen_date</option> + <option value="length">length</option> + <option value="md5">md5</option> + <option value="n_citations">n_citations</option> + <option value="n_xrefs">n_xrefs</option> + <option value="name">name</option> + <option value="organelle">organelle</option> + <option value="popular_species">popular_species</option> + <option value="product">product</option> + <option value="pub_id">pub_id</option> + <option value="pub_title">pub_title</option> + <option value="rna_type">rna_type</option> + <option value="species">species</option> + </param> + <conditional name="comp_operation"> + <param name="operation" type="select" label="Comparison operation" > + <option value="equal">equal</option> + <option value="not">not</option> + <option value="range">range</option> + </param> + <when value="equal"> + <param name="query_text" type="text" label="Searched term"/> + </when> + <when value="not"> + <param name="query_text" type="text" label="Searched term"/> + <param name="not_query_text" type="text" label="Limiting term"/> + </when> + <when value="range"> + <param name="min" type="text" label="From"/> + <param name="max" type="text" label="To"/> + </when> + </conditional> + </repeat> + </when> + + <when value="reactome"> + <param name="fields" type="select" label="Fields to extract" multiple="true"> + <option value="ARACYC" selected="true">ARACYC</option> + <option value="BIOMODELS_DATABASE" selected="true">BIOMODELS_DATABASE</option> + <option value="CAS" selected="true">CAS</option> + <option value="CHEBI" selected="true">CHEBI</option> + <option value="COMPOUND" selected="true">COMPOUND</option> + <option value="COSMIC" selected="true">COSMIC</option> + <option value="DOCK_BLASTER" selected="true">DOCK_BLASTER</option> + <option value="DOID" selected="true">DOID</option> + <option value="EC" selected="true">EC</option> + <option value="EMBL" selected="true">EMBL</option> + <option value="ENSEMBL" selected="true">ENSEMBL</option> + <option value="GENECARDS" selected="true">GENECARDS</option> + <option value="GO" selected="true">GO</option> + <option value="HMDB_METABOLITE" selected="true">HMDB_METABOLITE</option> + <option value="HMDB_PROTEIN" selected="true">HMDB_PROTEIN</option> + <option value="INTACT" selected="true">INTACT</option> + <option value="KEGG_GENE" selected="true">KEGG_GENE</option> + <option value="KEGG_GLYCAN" selected="true">KEGG_GLYCAN</option> + <option value="KNAPSACK" selected="true">KNAPSACK</option> + <option value="MIRBASE" selected="true">MIRBASE</option> + <option value="NCBI_NUCLEOTIDE" selected="true">NCBI_NUCLEOTIDE</option> + <option value="NCBI_PROTEIN" selected="true">NCBI_PROTEIN</option> + <option value="OMIM" selected="true">OMIM</option> + <option value="PRF" selected="true">PRF</option> + <option value="PRO" selected="true">PRO</option> + <option value="PROTEIN_DATA_BANK" selected="true">PROTEIN_DATA_BANK</option> + <option value="PUBCHEM" selected="true">PUBCHEM</option> + <option value="PUBCHEM_COMPOUND" selected="true">PUBCHEM_COMPOUND</option> + <option value="PUBCHEM_SUBSTANCE" selected="true">PUBCHEM_SUBSTANCE</option> + <option value="PUBMED" selected="true">PUBMED</option> + <option value="REFSEQ" selected="true">REFSEQ</option> + <option value="RHEA" selected="true">RHEA</option> + <option value="RICECYC" selected="true">RICECYC</option> + <option value="SVENCYC" selected="true">SVENCYC</option> + <option value="TAXONOMY" selected="true">TAXONOMY</option> + <option value="UCSC_HUMAN" selected="true">UCSC_HUMAN</option> + <option value="UNIPROT" selected="true">UNIPROT</option> + <option value="WIKIPEDIA" selected="true">WIKIPEDIA</option> + <option value="ZINC" selected="true">ZINC</option> + <option value="ZINC_TARGET" selected="true">ZINC_TARGET</option> + <option value="description" selected="true">description</option> + <option value="domain_source" selected="true">domain_source</option> + <option value="external_reference_other_identifier" selected="true">external_reference_other_identifier</option> + <option value="id" selected="true">id</option> + <option value="inferred_summation" selected="true">inferred_summation</option> + <option value="name" selected="true">name</option> + <option value="species" selected="true">species</option> + <option value="stid" selected="true">stid</option> + <option value="type" selected="true">type</option> + <validator type="no_options" message="Please select at least one field" /> + </param> + <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> + <param name="query_field" type="select" label="Fields" > + <option value="ARACYC">ARACYC</option> + <option value="BIOMODELS_DATABASE">BIOMODELS_DATABASE</option> + <option value="CAS">CAS</option> + <option value="CHEBI">CHEBI</option> + <option value="COMPOUND">COMPOUND</option> + <option value="COSMIC">COSMIC</option> + <option value="DOCK_BLASTER">DOCK_BLASTER</option> + <option value="DOID">DOID</option> + <option value="EC">EC</option> + <option value="EMBL">EMBL</option> + <option value="ENSEMBL">ENSEMBL</option> + <option value="GENECARDS">GENECARDS</option> + <option value="GO">GO</option> + <option value="HMDB_METABOLITE">HMDB_METABOLITE</option> + <option value="HMDB_PROTEIN">HMDB_PROTEIN</option> + <option value="INTACT">INTACT</option> + <option value="KEGG_GENE">KEGG_GENE</option> + <option value="KEGG_GLYCAN">KEGG_GLYCAN</option> + <option value="KNAPSACK">KNAPSACK</option> + <option value="MIRBASE">MIRBASE</option> + <option value="NCBI_NUCLEOTIDE">NCBI_NUCLEOTIDE</option> + <option value="NCBI_PROTEIN">NCBI_PROTEIN</option> + <option value="OMIM">OMIM</option> + <option value="PRF">PRF</option> + <option value="PRO">PRO</option> + <option value="PROTEIN_DATA_BANK">PROTEIN_DATA_BANK</option> + <option value="PUBCHEM">PUBCHEM</option> + <option value="PUBCHEM_COMPOUND">PUBCHEM_COMPOUND</option> + <option value="PUBCHEM_SUBSTANCE">PUBCHEM_SUBSTANCE</option> + <option value="PUBMED">PUBMED</option> + <option value="REFSEQ">REFSEQ</option> + <option value="RHEA">RHEA</option> + <option value="RICECYC">RICECYC</option> + <option value="SVENCYC">SVENCYC</option> + <option value="TAXONOMY">TAXONOMY</option> + <option value="UCSC_HUMAN">UCSC_HUMAN</option> + <option value="UNIPROT">UNIPROT</option> + <option value="WIKIPEDIA">WIKIPEDIA</option> + <option value="ZINC">ZINC</option> + <option value="ZINC_TARGET">ZINC_TARGET</option> + <option value="compartment_name">compartment_name</option> + <option value="description">description</option> + <option value="disease_name">disease_name</option> + <option value="disease_synonym">disease_synonym</option> + <option value="domain_source">domain_source</option> + <option value="external_reference_name">external_reference_name</option> + <option value="external_reference_other_identifier">external_reference_other_identifier</option> + <option value="external_reference_synonym">external_reference_synonym</option> + <option value="gene_names">gene_names</option> + <option value="go_biological_process_name">go_biological_process_name</option> + <option value="go_molecular_function_name">go_molecular_function_name</option> + <option value="id">id</option> + <option value="keyword">keyword</option> + <option value="literature_reference_title">literature_reference_title</option> + <option value="name">name</option> + <option value="oldstid">oldstid</option> + <option value="regulated_entity">regulated_entity</option> + <option value="regulator">regulator</option> + <option value="related_species">related_species</option> + <option value="species">species</option> + <option value="stid">stid</option> + <option value="synonym">synonym</option> + <option value="type">type</option> + </param> + <conditional name="comp_operation"> + <param name="operation" type="select" label="Comparison operation" > + <option value="equal">equal</option> + <option value="not">not</option> + <option value="range">range</option> + </param> + <when value="equal"> + <param name="query_text" type="text" label="Searched term"/> + </when> + <when value="not"> + <param name="query_text" type="text" label="Searched term"/> + <param name="not_query_text" type="text" label="Limiting term"/> + </when> + <when value="range"> + <param name="min" type="text" label="From"/> + <param name="max" type="text" label="To"/> + </when> + </conditional> + </repeat> + </when> + + <when value="sra-experiment"> + <param name="fields" type="select" label="Fields to extract" multiple="true"> + <option value="BIOSAMPLE" selected="true">BIOSAMPLE</option> + <option value="PROJECT" selected="true">PROJECT</option> + <option value="SAMPLE" selected="true">SAMPLE</option> + <option value="SRA-RUN" selected="true">SRA-RUN</option> + <option value="SRA-SAMPLE" selected="true">SRA-SAMPLE</option> + <option value="SRA-STUDY" selected="true">SRA-STUDY</option> + <option value="SRA-SUBMISSION" selected="true">SRA-SUBMISSION</option> + <option value="description" selected="true">description</option> + <option value="domain_source" selected="true">domain_source</option> + <option value="id" selected="true">id</option> + <validator type="no_options" message="Please select at least one field" /> + </param> + <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> + <param name="query_field" type="select" label="Fields" > + <option value="BIOSAMPLE">BIOSAMPLE</option> + <option value="PROJECT">PROJECT</option> + <option value="SAMPLE">SAMPLE</option> + <option value="SRA-RUN">SRA-RUN</option> + <option value="SRA-SAMPLE">SRA-SAMPLE</option> + <option value="SRA-STUDY">SRA-STUDY</option> + <option value="SRA-SUBMISSION">SRA-SUBMISSION</option> + <option value="abstract">abstract</option> + <option value="acc">acc</option> + <option value="alias">alias</option> + <option value="center_name">center_name</option> + <option value="description">description</option> + <option value="domain_source">domain_source</option> + <option value="id">id</option> + <option value="instrument_model">instrument_model</option> + <option value="library_name">library_name</option> + <option value="library_selection">library_selection</option> + <option value="library_source">library_source</option> + <option value="library_strategy">library_strategy</option> + </param> + <conditional name="comp_operation"> + <param name="operation" type="select" label="Comparison operation" > + <option value="equal">equal</option> + <option value="not">not</option> + <option value="range">range</option> + </param> + <when value="equal"> + <param name="query_text" type="text" label="Searched term"/> + </when> + <when value="not"> + <param name="query_text" type="text" label="Searched term"/> + <param name="not_query_text" type="text" label="Limiting term"/> + </when> + <when value="range"> + <param name="min" type="text" label="From"/> + <param name="max" type="text" label="To"/> + </when> + </conditional> + </repeat> + </when> + + <when value="sra-run"> + <param name="fields" type="select" label="Fields to extract" multiple="true"> + <option value="SRA-EXPERIMENT" selected="true">SRA-EXPERIMENT</option> + <option value="SRA-SAMPLE" selected="true">SRA-SAMPLE</option> + <option value="SRA-STUDY" selected="true">SRA-STUDY</option> + <option value="SRA-SUBMISSION" selected="true">SRA-SUBMISSION</option> + <option value="description" selected="true">description</option> + <option value="domain_source" selected="true">domain_source</option> + <option value="id" selected="true">id</option> + <validator type="no_options" message="Please select at least one field" /> + </param> + <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> + <param name="query_field" type="select" label="Fields" > + <option value="SRA-EXPERIMENT">SRA-EXPERIMENT</option> + <option value="SRA-SAMPLE">SRA-SAMPLE</option> + <option value="SRA-STUDY">SRA-STUDY</option> + <option value="SRA-SUBMISSION">SRA-SUBMISSION</option> + <option value="acc">acc</option> + <option value="alias">alias</option> + <option value="center_name">center_name</option> + <option value="description">description</option> + <option value="domain_source">domain_source</option> + <option value="id">id</option> + </param> + <conditional name="comp_operation"> + <param name="operation" type="select" label="Comparison operation" > + <option value="equal">equal</option> + <option value="not">not</option> + <option value="range">range</option> + </param> + <when value="equal"> + <param name="query_text" type="text" label="Searched term"/> + </when> + <when value="not"> + <param name="query_text" type="text" label="Searched term"/> + <param name="not_query_text" type="text" label="Limiting term"/> + </when> + <when value="range"> + <param name="min" type="text" label="From"/> + <param name="max" type="text" label="To"/> + </when> + </conditional> + </repeat> + </when> + + <when value="ebiweb_resources"> + <param name="fields" type="select" label="Fields to extract" multiple="true"> + <option value="description" selected="true">description</option> + <option value="domain_source" selected="true">domain_source</option> + <option value="id" selected="true">id</option> + <option value="logo" selected="true">logo</option> + <option value="name" selected="true">name</option> + <option value="short_name" selected="true">short_name</option> + <option value="thumbnail" selected="true">thumbnail</option> + <option value="url" selected="true">url</option> + <validator type="no_options" message="Please select at least one field" /> + </param> + <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> + <param name="query_field" type="select" label="Fields" > + <option value="activity">activity</option> + <option value="category">category</option> + <option value="cluster">cluster</option> + <option value="description">description</option> + <option value="domain">domain</option> + <option value="domain_source">domain_source</option> + <option value="id">id</option> + <option value="keywords">keywords</option> + <option value="long_description">long_description</option> + <option value="name">name</option> + <option value="short_name">short_name</option> + </param> + <conditional name="comp_operation"> + <param name="operation" type="select" label="Comparison operation" > + <option value="equal">equal</option> + <option value="not">not</option> + <option value="range">range</option> + </param> + <when value="equal"> + <param name="query_text" type="text" label="Searched term"/> + </when> + <when value="not"> + <param name="query_text" type="text" label="Searched term"/> + <param name="not_query_text" type="text" label="Limiting term"/> + </when> + <when value="range"> + <param name="min" type="text" label="From"/> + <param name="max" type="text" label="To"/> + </when> + </conditional> + </repeat> + </when> + + <when value="rhea"> + <param name="fields" type="select" label="Fields to extract" multiple="true"> + <option value="CHEBI" selected="true">CHEBI</option> + <option value="CITATION" selected="true">CITATION</option> + <option value="ECOCYC" selected="true">ECOCYC</option> + <option value="INTENZ" selected="true">INTENZ</option> + <option value="KEGG_REACTION" selected="true">KEGG_REACTION</option> + <option value="MACIE" selected="true">MACIE</option> + <option value="METACYC" selected="true">METACYC</option> + <option value="REACTOME" selected="true">REACTOME</option> + <option value="UNIPATHWAY" selected="true">UNIPATHWAY</option> + <option value="UNIPROT" selected="true">UNIPROT</option> + <option value="acc" selected="true">acc</option> + <option value="chebiIdEquation" selected="true">chebiIdEquation</option> + <option value="domain_source" selected="true">domain_source</option> + <option value="id" selected="true">id</option> + <option value="name" selected="true">name</option> + <validator type="no_options" message="Please select at least one field" /> + </param> + <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> + <param name="query_field" type="select" label="Fields" > + <option value="CHEBI">CHEBI</option> + <option value="CITATION">CITATION</option> + <option value="ECOCYC">ECOCYC</option> + <option value="INTENZ">INTENZ</option> + <option value="KEGG_REACTION">KEGG_REACTION</option> + <option value="MACIE">MACIE</option> + <option value="METACYC">METACYC</option> + <option value="REACTOME">REACTOME</option> + <option value="UNIPATHWAY">UNIPATHWAY</option> + <option value="UNIPROT">UNIPROT</option> + <option value="acc">acc</option> + <option value="comment">comment</option> + <option value="domain_source">domain_source</option> + <option value="id">id</option> + <option value="name">name</option> + </param> + <conditional name="comp_operation"> + <param name="operation" type="select" label="Comparison operation" > + <option value="equal">equal</option> + <option value="not">not</option> + <option value="range">range</option> + </param> + <when value="equal"> + <param name="query_text" type="text" label="Searched term"/> + </when> + <when value="not"> + <param name="query_text" type="text" label="Searched term"/> + <param name="not_query_text" type="text" label="Limiting term"/> + </when> + <when value="range"> + <param name="min" type="text" label="From"/> + <param name="max" type="text" label="To"/> + </when> + </conditional> + </repeat> + </when> + + <when value="sbo"> + <param name="fields" type="select" label="Fields to extract" multiple="true"> + <option value="SBO" selected="true">SBO</option> + <option value="description" selected="true">description</option> + <option value="domain_source" selected="true">domain_source</option> + <option value="id" selected="true">id</option> + <option value="name" selected="true">name</option> + <validator type="no_options" message="Please select at least one field" /> + </param> + <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> + <param name="query_field" type="select" label="Fields" > + <option value="SBO">SBO</option> + <option value="comment">comment</option> + <option value="description">description</option> + <option value="domain_source">domain_source</option> + <option value="id">id</option> + <option value="name">name</option> + <option value="namespace">namespace</option> + <option value="synonym">synonym</option> + </param> + <conditional name="comp_operation"> + <param name="operation" type="select" label="Comparison operation" > + <option value="equal">equal</option> + <option value="not">not</option> + <option value="range">range</option> + </param> + <when value="equal"> + <param name="query_text" type="text" label="Searched term"/> + </when> + <when value="not"> + <param name="query_text" type="text" label="Searched term"/> + <param name="not_query_text" type="text" label="Limiting term"/> + </when> + <when value="range"> + <param name="min" type="text" label="From"/> + <param name="max" type="text" label="To"/> + </when> + </conditional> + </repeat> + </when> + + <when value="sra-sample"> + <param name="fields" type="select" label="Fields to extract" multiple="true"> + <option value="BIOSAMPLE" selected="true">BIOSAMPLE</option> + <option value="SRA-SUBMISSION" selected="true">SRA-SUBMISSION</option> + <option value="TAXON" selected="true">TAXON</option> + <option value="acc" selected="true">acc</option> + <option value="common_name" selected="true">common_name</option> + <option value="description" selected="true">description</option> + <option value="domain_source" selected="true">domain_source</option> + <option value="id" selected="true">id</option> + <option value="scientific_name" selected="true">scientific_name</option> + <validator type="no_options" message="Please select at least one field" /> + </param> + <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> + <param name="query_field" type="select" label="Fields" > + <option value="BIOSAMPLE">BIOSAMPLE</option> + <option value="ENA-CHECKLIST">ENA-CHECKLIST</option> + <option value="SRA-SUBMISSION">SRA-SUBMISSION</option> + <option value="TAXON">TAXON</option> + <option value="abstract">abstract</option> + <option value="acc">acc</option> + <option value="alias">alias</option> + <option value="center_name">center_name</option> + <option value="common_name">common_name</option> + <option value="description">description</option> + <option value="domain_source">domain_source</option> + <option value="id">id</option> + <option value="keywords">keywords</option> + <option value="scientific_name">scientific_name</option> + <option value="secondary_id">secondary_id</option> + </param> + <conditional name="comp_operation"> + <param name="operation" type="select" label="Comparison operation" > + <option value="equal">equal</option> + <option value="not">not</option> + <option value="range">range</option> + </param> + <when value="equal"> + <param name="query_text" type="text" label="Searched term"/> + </when> + <when value="not"> + <param name="query_text" type="text" label="Searched term"/> + <param name="not_query_text" type="text" label="Limiting term"/> + </when> + <when value="range"> + <param name="min" type="text" label="From"/> + <param name="max" type="text" label="To"/> + </when> + </conditional> + </repeat> + </when> + + <when value="emblrelease_standard"> + <param name="fields" type="select" label="Fields to extract" multiple="true"> + <option value="AGRICOLA" selected="true">AGRICOLA</option> + <option value="BIOSAMPLE" selected="true">BIOSAMPLE</option> + <option value="CABRI" selected="true">CABRI</option> + <option value="CCAP" selected="true">CCAP</option> + <option value="COMPARE-REFGENOME" selected="true">COMPARE-REFGENOME</option> + <option value="DOI" selected="true">DOI</option> + <option value="EC" selected="true">EC</option> + <option value="EMBL-TSA" selected="true">EMBL-TSA</option> + <option value="EMBLCDS" selected="true">EMBLCDS</option> + <option value="ENA" selected="true">ENA</option> + <option value="ENA-CON" selected="true">ENA-CON</option> + <option value="ENSEMBL-GN" selected="true">ENSEMBL-GN</option> + <option value="ENSEMBLGENOMES-GN" selected="true">ENSEMBLGENOMES-GN</option> + <option value="EPD" selected="true">EPD</option> + <option value="EUROPEPMC" selected="true">EUROPEPMC</option> + <option value="FLYBASE" selected="true">FLYBASE</option> + <option value="GENEDB" selected="true">GENEDB</option> + <option value="GOA" selected="true">GOA</option> + <option value="GRAINGENES" selected="true">GRAINGENES</option> + <option value="GTRNADB" selected="true">GTRNADB</option> + <option value="H-INVDB" selected="true">H-INVDB</option> + <option value="HGNC" selected="true">HGNC</option> + <option value="INTERPRO" selected="true">INTERPRO</option> + <option value="IPD-KIR" selected="true">IPD-KIR</option> + <option value="IPD-MHC" selected="true">IPD-MHC</option> + <option value="ISHAM-ITS" selected="true">ISHAM-ITS</option> + <option value="LNCRNADB" selected="true">LNCRNADB</option> + <option value="MGI" selected="true">MGI</option> + <option value="MIRBASE" selected="true">MIRBASE</option> + <option value="PATENT_NUMBER" selected="true">PATENT_NUMBER</option> + <option value="PDB" selected="true">PDB</option> + <option value="PLNCDB" selected="true">PLNCDB</option> + <option value="POMBASE" selected="true">POMBASE</option> + <option value="PUBMED" selected="true">PUBMED</option> + <option value="RFAM" selected="true">RFAM</option> + <option value="SGD" selected="true">SGD</option> + <option value="SILVA-LSU" selected="true">SILVA-LSU</option> + <option value="SILVA-SSU" selected="true">SILVA-SSU</option> + <option value="SNOPYDB" selected="true">SNOPYDB</option> + <option value="SRPDB" selected="true">SRPDB</option> + <option value="STRAININFO" selected="true">STRAININFO</option> + <option value="SUBTILIST" selected="true">SUBTILIST</option> + <option value="TAIR" selected="true">TAIR</option> + <option value="TAXON" selected="true">TAXON</option> + <option value="TMRNA-WEBSITE" selected="true">TMRNA-WEBSITE</option> + <option value="UNILIB" selected="true">UNILIB</option> + <option value="UNIPROTKB_SWISS-PROT" selected="true">UNIPROTKB_SWISS-PROT</option> + <option value="UNIPROTKB_TREMBL" selected="true">UNIPROTKB_TREMBL</option> + <option value="UNITE" selected="true">UNITE</option> + <option value="VBASE2" selected="true">VBASE2</option> + <option value="VEGA-GN" selected="true">VEGA-GN</option> + <option value="VEGA-TR" selected="true">VEGA-TR</option> + <option value="WORMBASE" selected="true">WORMBASE</option> + <option value="ZFIN" selected="true">ZFIN</option> + <option value="acc" selected="true">acc</option> + <option value="description" selected="true">description</option> + <option value="domain_source" selected="true">domain_source</option> + <option value="id" selected="true">id</option> + <validator type="no_options" message="Please select at least one field" /> + </param> + <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> + <param name="query_field" type="select" label="Fields" > + <option value="AGRICOLA">AGRICOLA</option> + <option value="BIOSAMPLE">BIOSAMPLE</option> + <option value="CABRI">CABRI</option> + <option value="CCAP">CCAP</option> + <option value="COMPARE-REFGENOME">COMPARE-REFGENOME</option> + <option value="DOI">DOI</option> + <option value="EC">EC</option> + <option value="EMBL-TSA">EMBL-TSA</option> + <option value="EMBLCDS">EMBLCDS</option> + <option value="EMBLCDS_version">EMBLCDS_version</option> + <option value="ENA">ENA</option> + <option value="ENA-CON">ENA-CON</option> + <option value="ENSEMBL-GN">ENSEMBL-GN</option> + <option value="ENSEMBL-SCAFFOLDS">ENSEMBL-SCAFFOLDS</option> + <option value="ENSEMBL-TR">ENSEMBL-TR</option> + <option value="ENSEMBLGENOMES-GN">ENSEMBLGENOMES-GN</option> + <option value="ENSEMBLGENOMES-TR">ENSEMBLGENOMES-TR</option> + <option value="EPD">EPD</option> + <option value="EUROPEPMC">EUROPEPMC</option> + <option value="FLYBASE">FLYBASE</option> + <option value="GENEDB">GENEDB</option> + <option value="GOA">GOA</option> + <option value="GRAINGENES">GRAINGENES</option> + <option value="GTRNADB">GTRNADB</option> + <option value="H-INVDB">H-INVDB</option> + <option value="HGNC">HGNC</option> + <option value="IMGT_HLA">IMGT_HLA</option> + <option value="IMGT_LIGM">IMGT_LIGM</option> + <option value="INTERPRO">INTERPRO</option> + <option value="IPD-KIR">IPD-KIR</option> + <option value="IPD-MHC">IPD-MHC</option> + <option value="ISHAM-ITS">ISHAM-ITS</option> + <option value="LNCRNADB">LNCRNADB</option> + <option value="MD5">MD5</option> + <option value="MGI">MGI</option> + <option value="MIRBASE">MIRBASE</option> + <option value="PATENT_NUMBER">PATENT_NUMBER</option> + <option value="PDB">PDB</option> + <option value="PLNCDB">PLNCDB</option> + <option value="POMBASE">POMBASE</option> + <option value="PR2">PR2</option> + <option value="PROJECT">PROJECT</option> + <option value="PSEUDO">PSEUDO</option> + <option value="PUBMED">PUBMED</option> + <option value="RFAM">RFAM</option> + <option value="SGD">SGD</option> + <option value="SILVA-LSU">SILVA-LSU</option> + <option value="SILVA-SSU">SILVA-SSU</option> + <option value="SNOPYDB">SNOPYDB</option> + <option value="SRPDB">SRPDB</option> + <option value="STRAININFO">STRAININFO</option> + <option value="SUBTILIST">SUBTILIST</option> + <option value="TAIR">TAIR</option> + <option value="TAXON">TAXON</option> + <option value="TMRNA-WEBSITE">TMRNA-WEBSITE</option> + <option value="UNILIB">UNILIB</option> + <option value="UNIPROTKB_SWISS-PROT">UNIPROTKB_SWISS-PROT</option> + <option value="UNIPROTKB_TREMBL">UNIPROTKB_TREMBL</option> + <option value="UNITE">UNITE</option> + <option value="VBASE2">VBASE2</option> + <option value="VEGA-GN">VEGA-GN</option> + <option value="VEGA-TR">VEGA-TR</option> + <option value="WORMBASE">WORMBASE</option> + <option value="ZFIN">ZFIN</option> + <option value="acc">acc</option> + <option value="bio_material">bio_material</option> + <option value="creation_date">creation_date</option> + <option value="culture_collection">culture_collection</option> + <option value="data_class">data_class</option> + <option value="description">description</option> + <option value="division">division</option> + <option value="domain_source">domain_source</option> + <option value="gene">gene</option> + <option value="gene_synonym">gene_synonym</option> + <option value="id">id</option> + <option value="keywords">keywords</option> + <option value="last_modification_date">last_modification_date</option> + <option value="length">length</option> + <option value="locus_tag">locus_tag</option> + <option value="molecule_type">molecule_type</option> + <option value="old_locus_tag">old_locus_tag</option> + <option value="organelle">organelle</option> + <option value="organism">organism</option> + <option value="organism_classification">organism_classification</option> + <option value="organism_species">organism_species</option> + <option value="product">product</option> + <option value="references">references</option> + <option value="sequence_version">sequence_version</option> + <option value="specimen_voucher">specimen_voucher</option> + <option value="topology">topology</option> + </param> + <conditional name="comp_operation"> + <param name="operation" type="select" label="Comparison operation" > + <option value="equal">equal</option> + <option value="not">not</option> + <option value="range">range</option> + </param> + <when value="equal"> + <param name="query_text" type="text" label="Searched term"/> + </when> + <when value="not"> + <param name="query_text" type="text" label="Searched term"/> + <param name="not_query_text" type="text" label="Limiting term"/> + </when> + <when value="range"> + <param name="min" type="text" label="From"/> + <param name="max" type="text" label="To"/> + </when> + </conditional> + </repeat> + </when> + + <when value="emblnew_standard"> + <param name="fields" type="select" label="Fields to extract" multiple="true"> + <option value="AGRICOLA" selected="true">AGRICOLA</option> + <option value="BIOSAMPLE" selected="true">BIOSAMPLE</option> + <option value="CABRI" selected="true">CABRI</option> + <option value="COMPARE-REFGENOME" selected="true">COMPARE-REFGENOME</option> + <option value="DOI" selected="true">DOI</option> + <option value="EC" selected="true">EC</option> + <option value="EMBLCDS" selected="true">EMBLCDS</option> + <option value="ENA" selected="true">ENA</option> + <option value="ENA-CON" selected="true">ENA-CON</option> + <option value="ENSEMBL-GN" selected="true">ENSEMBL-GN</option> + <option value="ENSEMBLGENOMES-GN" selected="true">ENSEMBLGENOMES-GN</option> + <option value="EPD" selected="true">EPD</option> + <option value="EUROPEPMC" selected="true">EUROPEPMC</option> + <option value="FLYBASE" selected="true">FLYBASE</option> + <option value="GOA" selected="true">GOA</option> + <option value="GRAINGENES" selected="true">GRAINGENES</option> + <option value="H-INVDB" selected="true">H-INVDB</option> + <option value="HGNC" selected="true">HGNC</option> + <option value="INTERPRO" selected="true">INTERPRO</option> + <option value="IPD-MHC" selected="true">IPD-MHC</option> + <option value="MGI" selected="true">MGI</option> + <option value="PATENT_NUMBER" selected="true">PATENT_NUMBER</option> + <option value="PDB" selected="true">PDB</option> + <option value="PUBMED" selected="true">PUBMED</option> + <option value="RFAM" selected="true">RFAM</option> + <option value="SGD" selected="true">SGD</option> + <option value="SILVA-LSU" selected="true">SILVA-LSU</option> + <option value="SILVA-SSU" selected="true">SILVA-SSU</option> + <option value="STRAININFO" selected="true">STRAININFO</option> + <option value="TAIR" selected="true">TAIR</option> + <option value="TAXON" selected="true">TAXON</option> + <option value="UNIPROTKB_SWISS-PROT" selected="true">UNIPROTKB_SWISS-PROT</option> + <option value="UNIPROTKB_TREMBL" selected="true">UNIPROTKB_TREMBL</option> + <option value="UNITE" selected="true">UNITE</option> + <option value="ZFIN" selected="true">ZFIN</option> + <option value="acc" selected="true">acc</option> + <option value="description" selected="true">description</option> + <option value="domain_source" selected="true">domain_source</option> + <option value="id" selected="true">id</option> + <validator type="no_options" message="Please select at least one field" /> + </param> + <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> + <param name="query_field" type="select" label="Fields" > + <option value="AGRICOLA">AGRICOLA</option> + <option value="BIOSAMPLE">BIOSAMPLE</option> + <option value="CABRI">CABRI</option> + <option value="COMPARE-REFGENOME">COMPARE-REFGENOME</option> + <option value="DOI">DOI</option> + <option value="EC">EC</option> + <option value="EMBLCDS">EMBLCDS</option> + <option value="EMBLCDS_version">EMBLCDS_version</option> + <option value="ENA">ENA</option> + <option value="ENA-CON">ENA-CON</option> + <option value="ENSEMBL-GN">ENSEMBL-GN</option> + <option value="ENSEMBL-SCAFFOLDS">ENSEMBL-SCAFFOLDS</option> + <option value="ENSEMBL-TR">ENSEMBL-TR</option> + <option value="ENSEMBLGENOMES-GN">ENSEMBLGENOMES-GN</option> + <option value="ENSEMBLGENOMES-TR">ENSEMBLGENOMES-TR</option> + <option value="EPD">EPD</option> + <option value="EUROPEPMC">EUROPEPMC</option> + <option value="FLYBASE">FLYBASE</option> + <option value="GOA">GOA</option> + <option value="GRAINGENES">GRAINGENES</option> + <option value="H-INVDB">H-INVDB</option> + <option value="HGNC">HGNC</option> + <option value="IMGT_HLA">IMGT_HLA</option> + <option value="IMGT_LIGM">IMGT_LIGM</option> + <option value="INTERPRO">INTERPRO</option> + <option value="IPD-MHC">IPD-MHC</option> + <option value="MD5">MD5</option> + <option value="MGI">MGI</option> + <option value="PATENT_NUMBER">PATENT_NUMBER</option> + <option value="PDB">PDB</option> + <option value="PR2">PR2</option> + <option value="PROJECT">PROJECT</option> + <option value="PSEUDO">PSEUDO</option> + <option value="PUBMED">PUBMED</option> + <option value="RFAM">RFAM</option> + <option value="SGD">SGD</option> + <option value="SILVA-LSU">SILVA-LSU</option> + <option value="SILVA-SSU">SILVA-SSU</option> + <option value="STRAININFO">STRAININFO</option> + <option value="TAIR">TAIR</option> + <option value="TAXON">TAXON</option> + <option value="UNIPROTKB_SWISS-PROT">UNIPROTKB_SWISS-PROT</option> + <option value="UNIPROTKB_TREMBL">UNIPROTKB_TREMBL</option> + <option value="UNITE">UNITE</option> + <option value="ZFIN">ZFIN</option> + <option value="acc">acc</option> + <option value="bio_material">bio_material</option> + <option value="creation_date">creation_date</option> + <option value="culture_collection">culture_collection</option> + <option value="data_class">data_class</option> + <option value="description">description</option> + <option value="division">division</option> + <option value="domain_source">domain_source</option> + <option value="gene">gene</option> + <option value="gene_synonym">gene_synonym</option> + <option value="id">id</option> + <option value="keywords">keywords</option> + <option value="last_modification_date">last_modification_date</option> + <option value="length">length</option> + <option value="locus_tag">locus_tag</option> + <option value="molecule_type">molecule_type</option> + <option value="old_locus_tag">old_locus_tag</option> + <option value="organelle">organelle</option> + <option value="organism">organism</option> + <option value="organism_classification">organism_classification</option> + <option value="organism_species">organism_species</option> + <option value="product">product</option> + <option value="references">references</option> + <option value="sequence_version">sequence_version</option> + <option value="specimen_voucher">specimen_voucher</option> + <option value="topology">topology</option> + </param> + <conditional name="comp_operation"> + <param name="operation" type="select" label="Comparison operation" > + <option value="equal">equal</option> + <option value="not">not</option> + <option value="range">range</option> + </param> + <when value="equal"> + <param name="query_text" type="text" label="Searched term"/> + </when> + <when value="not"> + <param name="query_text" type="text" label="Searched term"/> + <param name="not_query_text" type="text" label="Limiting term"/> + </when> + <when value="range"> + <param name="min" type="text" label="From"/> + <param name="max" type="text" label="To"/> + </when> + </conditional> + </repeat> + </when> + + <when value="ebiweb_corporate"> + <param name="fields" type="select" label="Fields to extract" multiple="true"> + <option value="content" selected="true">content</option> + <option value="content_signature" selected="true">content_signature</option> + <option value="description" selected="true">description</option> + <option value="domain_source" selected="true">domain_source</option> + <option value="id" selected="true">id</option> + <option value="mime_type" selected="true">mime_type</option> + <option value="name" selected="true">name</option> + <option value="namespace" selected="true">namespace</option> + <validator type="no_options" message="Please select at least one field" /> + </param> + <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> + <param name="query_field" type="select" label="Fields" > + <option value="author">author</option> + <option value="content">content</option> + <option value="content_signature">content_signature</option> + <option value="creation_date">creation_date</option> + <option value="description">description</option> + <option value="domain_source">domain_source</option> + <option value="encoding">encoding</option> + <option value="id">id</option> + <option value="keywords">keywords</option> + <option value="last_modification_date">last_modification_date</option> + <option value="menu">menu</option> + <option value="mime_type">mime_type</option> + <option value="name">name</option> + <option value="namespace">namespace</option> + </param> + <conditional name="comp_operation"> + <param name="operation" type="select" label="Comparison operation" > + <option value="equal">equal</option> + <option value="not">not</option> + <option value="range">range</option> + </param> + <when value="equal"> + <param name="query_text" type="text" label="Searched term"/> + </when> + <when value="not"> + <param name="query_text" type="text" label="Searched term"/> + <param name="not_query_text" type="text" label="Limiting term"/> + </when> + <when value="range"> + <param name="min" type="text" label="From"/> + <param name="max" type="text" label="To"/> + </when> + </conditional> + </repeat> + </when> + + <when value="project"> + <param name="fields" type="select" label="Fields to extract" multiple="true"> + <option value="PUBMED" selected="true">PUBMED</option> + <option value="TAXON" selected="true">TAXON</option> + <option value="description" selected="true">description</option> + <option value="domain_source" selected="true">domain_source</option> + <option value="id" selected="true">id</option> + <option value="name" selected="true">name</option> + <validator type="no_options" message="Please select at least one field" /> + </param> + <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> + <param name="query_field" type="select" label="Fields" > + <option value="PUBMED">PUBMED</option> + <option value="TAXON">TAXON</option> + <option value="acc">acc</option> + <option value="description">description</option> + <option value="domain_source">domain_source</option> + <option value="id">id</option> + <option value="long_description">long_description</option> + <option value="name">name</option> + <option value="scientific_name">scientific_name</option> + <option value="strain">strain</option> + </param> + <conditional name="comp_operation"> + <param name="operation" type="select" label="Comparison operation" > + <option value="equal">equal</option> + <option value="not">not</option> + <option value="range">range</option> + </param> + <when value="equal"> + <param name="query_text" type="text" label="Searched term"/> + </when> + <when value="not"> + <param name="query_text" type="text" label="Searched term"/> + <param name="not_query_text" type="text" label="Limiting term"/> + </when> + <when value="range"> + <param name="min" type="text" label="From"/> + <param name="max" type="text" label="To"/> + </when> + </conditional> + </repeat> + </when> + + <when value="sra-study"> + <param name="fields" type="select" label="Fields to extract" multiple="true"> + <option value="PROJECT" selected="true">PROJECT</option> + <option value="PUBMED" selected="true">PUBMED</option> + <option value="SRA-STUDY" selected="true">SRA-STUDY</option> + <option value="SRA-SUBMISSION" selected="true">SRA-SUBMISSION</option> + <option value="description" selected="true">description</option> + <option value="domain_source" selected="true">domain_source</option> + <option value="existing_study_type" selected="true">existing_study_type</option> + <option value="id" selected="true">id</option> + <option value="new_study_type" selected="true">new_study_type</option> + <validator type="no_options" message="Please select at least one field" /> + </param> + <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> + <param name="query_field" type="select" label="Fields" > + <option value="PROJECT">PROJECT</option> + <option value="PUBMED">PUBMED</option> + <option value="SRA-STUDY">SRA-STUDY</option> + <option value="SRA-SUBMISSION">SRA-SUBMISSION</option> + <option value="abstract">abstract</option> + <option value="acc">acc</option> + <option value="alias">alias</option> + <option value="center_name">center_name</option> + <option value="center_project_name">center_project_name</option> + <option value="description">description</option> + <option value="domain_source">domain_source</option> + <option value="existing_study_type">existing_study_type</option> + <option value="id">id</option> + <option value="new_study_type">new_study_type</option> + </param> + <conditional name="comp_operation"> + <param name="operation" type="select" label="Comparison operation" > + <option value="equal">equal</option> + <option value="not">not</option> + <option value="range">range</option> + </param> + <when value="equal"> + <param name="query_text" type="text" label="Searched term"/> + </when> + <when value="not"> + <param name="query_text" type="text" label="Searched term"/> + <param name="not_query_text" type="text" label="Limiting term"/> + </when> + <when value="range"> + <param name="min" type="text" label="From"/> + <param name="max" type="text" label="To"/> + </when> + </conditional> + </repeat> + </when> + + <when value="sra-submission"> + <param name="fields" type="select" label="Fields to extract" multiple="true"> + <option value="description" selected="true">description</option> + <option value="domain_source" selected="true">domain_source</option> + <option value="id" selected="true">id</option> + <validator type="no_options" message="Please select at least one field" /> + </param> + <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> + <param name="query_field" type="select" label="Fields" > + <option value="acc">acc</option> + <option value="alias">alias</option> + <option value="center_name">center_name</option> + <option value="description">description</option> + <option value="domain_source">domain_source</option> + <option value="id">id</option> + </param> + <conditional name="comp_operation"> + <param name="operation" type="select" label="Comparison operation" > + <option value="equal">equal</option> + <option value="not">not</option> + <option value="range">range</option> + </param> + <when value="equal"> + <param name="query_text" type="text" label="Searched term"/> + </when> + <when value="not"> + <param name="query_text" type="text" label="Searched term"/> + <param name="not_query_text" type="text" label="Limiting term"/> + </when> + <when value="range"> + <param name="min" type="text" label="From"/> + <param name="max" type="text" label="To"/> + </when> + </conditional> + </repeat> + </when> + + <when value="taxonomy"> + <param name="fields" type="select" label="Fields to extract" multiple="true"> + <option value="TAXONOMY" selected="true">TAXONOMY</option> + <option value="acronym" selected="true">acronym</option> + <option value="anamorph" selected="true">anamorph</option> + <option value="blast_name" selected="true">blast_name</option> + <option value="common_name" selected="true">common_name</option> + <option value="doc_file" selected="true">doc_file</option> + <option value="domain_source" selected="true">domain_source</option> + <option value="equivalent_name" selected="true">equivalent_name</option> + <option value="genbank_acronym" selected="true">genbank_acronym</option> + <option value="genbank_anamorph" selected="true">genbank_anamorph</option> + <option value="genbank_common_name" selected="true">genbank_common_name</option> + <option value="genbank_synonym" selected="true">genbank_synonym</option> + <option value="id" selected="true">id</option> + <option value="name" selected="true">name</option> + <option value="offset_end" selected="true">offset_end</option> + <option value="offset_start" selected="true">offset_start</option> + <option value="synonym" selected="true">synonym</option> + <validator type="no_options" message="Please select at least one field" /> + </param> + <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> + <param name="query_field" type="select" label="Fields" > + <option value="TAXONOMY">TAXONOMY</option> + <option value="acronym">acronym</option> + <option value="anamorph">anamorph</option> + <option value="blast_name">blast_name</option> + <option value="common_name">common_name</option> + <option value="domain_source">domain_source</option> + <option value="equivalent_name">equivalent_name</option> + <option value="genbank_acronym">genbank_acronym</option> + <option value="genbank_anamorph">genbank_anamorph</option> + <option value="genbank_common_name">genbank_common_name</option> + <option value="genbank_synonym">genbank_synonym</option> + <option value="gene_code">gene_code</option> + <option value="id">id</option> + <option value="in_part">in_part</option> + <option value="includes">includes</option> + <option value="misnomer">misnomer</option> + <option value="misspelling">misspelling</option> + <option value="name">name</option> + <option value="rank">rank</option> + <option value="synonym">synonym</option> + <option value="teleomorph">teleomorph</option> + </param> + <conditional name="comp_operation"> + <param name="operation" type="select" label="Comparison operation" > + <option value="equal">equal</option> + <option value="not">not</option> + <option value="range">range</option> + </param> + <when value="equal"> + <param name="query_text" type="text" label="Searched term"/> + </when> + <when value="not"> + <param name="query_text" type="text" label="Searched term"/> + <param name="not_query_text" type="text" label="Limiting term"/> + </when> + <when value="range"> + <param name="min" type="text" label="From"/> + <param name="max" type="text" label="To"/> + </when> + </conditional> + </repeat> + </when> + + <when value="tsa_masters"> + <param name="fields" type="select" label="Fields to extract" multiple="true"> + <option value="BIOSAMPLE" selected="true">BIOSAMPLE</option> + <option value="PROJECT" selected="true">PROJECT</option> + <option value="PUBMED" selected="true">PUBMED</option> + <option value="SAMPLE" selected="true">SAMPLE</option> + <option value="TAXON" selected="true">TAXON</option> + <option value="acc" selected="true">acc</option> + <option value="description" selected="true">description</option> + <option value="domain_source" selected="true">domain_source</option> + <option value="id" selected="true">id</option> + <validator type="no_options" message="Please select at least one field" /> + </param> + <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> + <param name="query_field" type="select" label="Fields" > + <option value="BIOSAMPLE">BIOSAMPLE</option> + <option value="PROJECT">PROJECT</option> + <option value="PUBMED">PUBMED</option> + <option value="SAMPLE">SAMPLE</option> + <option value="TAXON">TAXON</option> + <option value="acc">acc</option> + <option value="bio_material">bio_material</option> + <option value="common_name">common_name</option> + <option value="creation_date">creation_date</option> + <option value="culture_collection">culture_collection</option> + <option value="description">description</option> + <option value="division">division</option> + <option value="domain_source">domain_source</option> + <option value="host">host</option> + <option value="id">id</option> + <option value="isolate">isolate</option> + <option value="isolation_source">isolation_source</option> + <option value="keywords">keywords</option> + <option value="last_modification_date">last_modification_date</option> + <option value="molecule_type">molecule_type</option> + <option value="prefix">prefix</option> + <option value="scientific_name">scientific_name</option> + <option value="specimen_voucher">specimen_voucher</option> + <option value="strain">strain</option> + </param> + <conditional name="comp_operation"> + <param name="operation" type="select" label="Comparison operation" > + <option value="equal">equal</option> + <option value="not">not</option> + <option value="range">range</option> + </param> + <when value="equal"> + <param name="query_text" type="text" label="Searched term"/> + </when> + <when value="not"> + <param name="query_text" type="text" label="Searched term"/> + <param name="not_query_text" type="text" label="Limiting term"/> + </when> + <when value="range"> + <param name="min" type="text" label="From"/> + <param name="max" type="text" label="To"/> + </when> + </conditional> + </repeat> + </when> + + <when value="treefam"> + <param name="fields" type="select" label="Fields to extract" multiple="true"> + <option value="ENSEMBL" selected="true">ENSEMBL</option> + <option value="HGNC" selected="true">HGNC</option> + <option value="PFAM" selected="true">PFAM</option> + <option value="TAXONOMY" selected="true">TAXONOMY</option> + <option value="UNIPROT" selected="true">UNIPROT</option> + <option value="WIKIGENE" selected="true">WIKIGENE</option> + <option value="description" selected="true">description</option> + <option value="domain_source" selected="true">domain_source</option> + <option value="id" selected="true">id</option> + <option value="name" selected="true">name</option> + <validator type="no_options" message="Please select at least one field" /> + </param> + <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> + <param name="query_field" type="select" label="Fields" > + <option value="ENSEMBL">ENSEMBL</option> + <option value="HGNC">HGNC</option> + <option value="PFAM">PFAM</option> + <option value="SCG">SCG</option> + <option value="TAXONOMY">TAXONOMY</option> + <option value="UNIPROT">UNIPROT</option> + <option value="WIKIGENE">WIKIGENE</option> + <option value="description">description</option> + <option value="domain_source">domain_source</option> + <option value="gene_symbol">gene_symbol</option> + <option value="gene_synonym">gene_synonym</option> + <option value="id">id</option> + <option value="name">name</option> + </param> + <conditional name="comp_operation"> + <param name="operation" type="select" label="Comparison operation" > + <option value="equal">equal</option> + <option value="not">not</option> + <option value="range">range</option> + </param> + <when value="equal"> + <param name="query_text" type="text" label="Searched term"/> + </when> + <when value="not"> + <param name="query_text" type="text" label="Searched term"/> + <param name="not_query_text" type="text" label="Limiting term"/> + </when> + <when value="range"> + <param name="min" type="text" label="From"/> + <param name="max" type="text" label="To"/> + </when> + </conditional> + </repeat> + </when> + + <when value="uspto"> + <param name="fields" type="select" label="Fields to extract" multiple="true"> + <option value="PATENT_NUMBER" selected="true">PATENT_NUMBER</option> + <option value="acc" selected="true">acc</option> + <option value="description" selected="true">description</option> + <option value="doc_file" selected="true">doc_file</option> + <option value="domain_source" selected="true">domain_source</option> + <option value="id" selected="true">id</option> + <option value="offset_end" selected="true">offset_end</option> + <option value="offset_start" selected="true">offset_start</option> + <validator type="no_options" message="Please select at least one field" /> + </param> + <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> + <param name="query_field" type="select" label="Fields" > + <option value="PATENT_NUMBER">PATENT_NUMBER</option> + <option value="acc">acc</option> + <option value="creation_date">creation_date</option> + <option value="data_class">data_class</option> + <option value="description">description</option> + <option value="domain_source">domain_source</option> + <option value="id">id</option> + <option value="length">length</option> + <option value="md5">md5</option> + <option value="organism">organism</option> + <option value="organism_species">organism_species</option> + <option value="references">references</option> + <option value="sequence_version">sequence_version</option> + </param> + <conditional name="comp_operation"> + <param name="operation" type="select" label="Comparison operation" > + <option value="equal">equal</option> + <option value="not">not</option> + <option value="range">range</option> + </param> + <when value="equal"> + <param name="query_text" type="text" label="Searched term"/> + </when> + <when value="not"> + <param name="query_text" type="text" label="Searched term"/> + <param name="not_query_text" type="text" label="Limiting term"/> + </when> + <when value="range"> + <param name="min" type="text" label="From"/> + <param name="max" type="text" label="To"/> + </when> + </conditional> + </repeat> + </when> + + <when value="uniparc"> + <param name="fields" type="select" label="Fields to extract" multiple="true"> + <option value="EMBL" selected="true">EMBL</option> + <option value="EMBLWGS" selected="true">EMBLWGS</option> + <option value="EMBL_CON" selected="true">EMBL_CON</option> + <option value="EMBL_TPA" selected="true">EMBL_TPA</option> + <option value="EMBL_TSA" selected="true">EMBL_TSA</option> + <option value="ENSEMBL" selected="true">ENSEMBL</option> + <option value="ENSEMBLBACTERIA" selected="true">ENSEMBLBACTERIA</option> + <option value="ENSEMBLFUNGI" selected="true">ENSEMBLFUNGI</option> + <option value="ENSEMBLMETAZOA" selected="true">ENSEMBLMETAZOA</option> + <option value="ENSEMBLPLANTS" selected="true">ENSEMBLPLANTS</option> + <option value="ENSEMBLPROTISTS" selected="true">ENSEMBLPROTISTS</option> + <option value="EPO" selected="true">EPO</option> + <option value="FLYBASE" selected="true">FLYBASE</option> + <option value="H-INVDB" selected="true">H-INVDB</option> + <option value="JPO" selected="true">JPO</option> + <option value="KIPO" selected="true">KIPO</option> + <option value="NCBI" selected="true">NCBI</option> + <option value="PATRIC" selected="true">PATRIC</option> + <option value="PDB" selected="true">PDB</option> + <option value="PRF" selected="true">PRF</option> + <option value="REFSEQ" selected="true">REFSEQ</option> + <option value="SEED" selected="true">SEED</option> + <option value="SGD" selected="true">SGD</option> + <option value="TAIR" selected="true">TAIR</option> + <option value="TAXONOMY" selected="true">TAXONOMY</option> + <option value="TROME" selected="true">TROME</option> + <option value="UNIPROT" selected="true">UNIPROT</option> + <option value="UNIPROTKB_SWISS-PROT" selected="true">UNIPROTKB_SWISS-PROT</option> + <option value="UNIPROTKB_SWISS-PROT_PROTEIN_ISOFORMS" selected="true">UNIPROTKB_SWISS-PROT_PROTEIN_ISOFORMS</option> + <option value="UNIPROTKB_TREMBL" selected="true">UNIPROTKB_TREMBL</option> + <option value="USPTO" selected="true">USPTO</option> + <option value="VECTORBASE" selected="true">VECTORBASE</option> + <option value="VEGA" selected="true">VEGA</option> + <option value="WBPARASITE" selected="true">WBPARASITE</option> + <option value="WORMBASE" selected="true">WORMBASE</option> + <option value="domain_source" selected="true">domain_source</option> + <option value="gene_name" selected="true">gene_name</option> + <option value="id" selected="true">id</option> + <option value="length" selected="true">length</option> + <validator type="no_options" message="Please select at least one field" /> + </param> + <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> + <param name="query_field" type="select" label="Fields" > + <option value="EMBL">EMBL</option> + <option value="EMBLWGS">EMBLWGS</option> + <option value="EMBL_CON">EMBL_CON</option> + <option value="EMBL_TPA">EMBL_TPA</option> + <option value="EMBL_TSA">EMBL_TSA</option> + <option value="ENSEMBL">ENSEMBL</option> + <option value="ENSEMBLBACTERIA">ENSEMBLBACTERIA</option> + <option value="ENSEMBLFUNGI">ENSEMBLFUNGI</option> + <option value="ENSEMBLMETAZOA">ENSEMBLMETAZOA</option> + <option value="ENSEMBLPLANTS">ENSEMBLPLANTS</option> + <option value="ENSEMBLPROTISTS">ENSEMBLPROTISTS</option> + <option value="EPO">EPO</option> + <option value="FLYBASE">FLYBASE</option> + <option value="H-INVDB">H-INVDB</option> + <option value="JPO">JPO</option> + <option value="KIPO">KIPO</option> + <option value="NCBI">NCBI</option> + <option value="PATRIC">PATRIC</option> + <option value="PDB">PDB</option> + <option value="PRF">PRF</option> + <option value="REFSEQ">REFSEQ</option> + <option value="SEED">SEED</option> + <option value="SGD">SGD</option> + <option value="TAIR">TAIR</option> + <option value="TAXONOMY">TAXONOMY</option> + <option value="TROME">TROME</option> + <option value="UNIPROT">UNIPROT</option> + <option value="UNIPROTKB_SWISS-PROT">UNIPROTKB_SWISS-PROT</option> + <option value="UNIPROTKB_SWISS-PROT_PROTEIN_ISOFORMS">UNIPROTKB_SWISS-PROT_PROTEIN_ISOFORMS</option> + <option value="UNIPROTKB_TREMBL">UNIPROTKB_TREMBL</option> + <option value="USPTO">USPTO</option> + <option value="VECTORBASE">VECTORBASE</option> + <option value="VEGA">VEGA</option> + <option value="WBPARASITE">WBPARASITE</option> + <option value="WORMBASE">WORMBASE</option> + <option value="crc64_iso">crc64_iso</option> + <option value="domain_source">domain_source</option> + <option value="gene_name">gene_name</option> + <option value="id">id</option> + <option value="length">length</option> + <option value="md5">md5</option> + <option value="pdb_chain">pdb_chain</option> + <option value="uniprotkb_exclusion">uniprotkb_exclusion</option> + </param> + <conditional name="comp_operation"> + <param name="operation" type="select" label="Comparison operation" > + <option value="equal">equal</option> + <option value="not">not</option> + <option value="range">range</option> + </param> + <when value="equal"> + <param name="query_text" type="text" label="Searched term"/> + </when> + <when value="not"> + <param name="query_text" type="text" label="Searched term"/> + <param name="not_query_text" type="text" label="Limiting term"/> + </when> + <when value="range"> + <param name="min" type="text" label="From"/> + <param name="max" type="text" label="To"/> + </when> + </conditional> + </repeat> + </when> + + <when value="uniprot"> + <param name="fields" type="select" label="Fields to extract" multiple="true"> + <option value="AGRICOLA" selected="true">AGRICOLA</option> + <option value="ALLERGOME" selected="true">ALLERGOME</option> + <option value="ARACHNOSERVER" selected="true">ARACHNOSERVER</option> + <option value="BGEE" selected="true">BGEE</option> + <option value="BINDINGDB" selected="true">BINDINGDB</option> + <option value="BIOCYC" selected="true">BIOCYC</option> + <option value="BIOGRID" selected="true">BIOGRID</option> + <option value="BIOMUTA" selected="true">BIOMUTA</option> + <option value="BRENDA" selected="true">BRENDA</option> + <option value="CAZY" selected="true">CAZY</option> + <option value="CCDS" selected="true">CCDS</option> + <option value="CDD" selected="true">CDD</option> + <option value="CGD" selected="true">CGD</option> + <option value="CHEBI" selected="true">CHEBI</option> + <option value="CHEMBL" selected="true">CHEMBL</option> + <option value="CHITARS" selected="true">CHITARS</option> + <option value="CLEANEX" selected="true">CLEANEX</option> + <option value="CODING" selected="true">CODING</option> + <option value="COLLECTF" selected="true">COLLECTF</option> + <option value="COMPLUYEAST-2DPAGE" selected="true">COMPLUYEAST-2DPAGE</option> + <option value="CONOSERVER" selected="true">CONOSERVER</option> + <option value="CTD" selected="true">CTD</option> + <option value="DEPOD" selected="true">DEPOD</option> + <option value="DI" selected="true">DI</option> + <option value="DICTYBASE" selected="true">DICTYBASE</option> + <option value="DIP" selected="true">DIP</option> + <option value="DISGENET" selected="true">DISGENET</option> + <option value="DISPROT" selected="true">DISPROT</option> + <option value="DMDM" selected="true">DMDM</option> + <option value="DNASU" selected="true">DNASU</option> + <option value="DOI" selected="true">DOI</option> + <option value="DOSAC-COBS-2DPAGE" selected="true">DOSAC-COBS-2DPAGE</option> + <option value="DRUGBANK" selected="true">DRUGBANK</option> + <option value="EC" selected="true">EC</option> + <option value="ECHOBASE" selected="true">ECHOBASE</option> + <option value="ECNUMBER" selected="true">ECNUMBER</option> + <option value="ECOGENE" selected="true">ECOGENE</option> + <option value="EGGNOG" selected="true">EGGNOG</option> + <option value="EMBL" selected="true">EMBL</option> + <option value="ENSEMBL" selected="true">ENSEMBL</option> + <option value="ENSEMBLBACTERIA" selected="true">ENSEMBLBACTERIA</option> + <option value="ENSEMBLFUNGI" selected="true">ENSEMBLFUNGI</option> + <option value="ENSEMBLMETAZOA" selected="true">ENSEMBLMETAZOA</option> + <option value="ENSEMBLPLANTS" selected="true">ENSEMBLPLANTS</option> + <option value="ENSEMBLPROTISTS" selected="true">ENSEMBLPROTISTS</option> + <option value="ENSEMBL_GENE" selected="true">ENSEMBL_GENE</option> + <option value="EPD" selected="true">EPD</option> + <option value="ESTHER" selected="true">ESTHER</option> + <option value="EUHCVDB" selected="true">EUHCVDB</option> + <option value="EUPATHDB" selected="true">EUPATHDB</option> + <option value="EVOLUTIONARYTRACE" selected="true">EVOLUTIONARYTRACE</option> + <option value="EXPRESSIONATLAS" selected="true">EXPRESSIONATLAS</option> + <option value="FLYBASE" selected="true">FLYBASE</option> + <option value="GENE3D" selected="true">GENE3D</option> + <option value="GENECARDS" selected="true">GENECARDS</option> + <option value="GENEDB" selected="true">GENEDB</option> + <option value="GENEID" selected="true">GENEID</option> + <option value="GENEREVIEWS" selected="true">GENEREVIEWS</option> + <option value="GENEVISIBLE" selected="true">GENEVISIBLE</option> + <option value="GENEWIKI" selected="true">GENEWIKI</option> + <option value="GENOMERNAI" selected="true">GENOMERNAI</option> + <option value="GO" selected="true">GO</option> + <option value="GRAMENE" selected="true">GRAMENE</option> + <option value="GUIDETOPHARMACOLOGY" selected="true">GUIDETOPHARMACOLOGY</option> + <option value="H-INVDB" selected="true">H-INVDB</option> + <option value="HAMAP" selected="true">HAMAP</option> + <option value="HAMAP-RULE" selected="true">HAMAP-RULE</option> + <option value="HGNC" selected="true">HGNC</option> + <option value="HOGENOM" selected="true">HOGENOM</option> + <option value="HOVERGEN" selected="true">HOVERGEN</option> + <option value="HPA" selected="true">HPA</option> + <option value="INPARANOID" selected="true">INPARANOID</option> + <option value="INTACT" selected="true">INTACT</option> + <option value="INTERPRO" selected="true">INTERPRO</option> + <option value="IPTMNET" selected="true">IPTMNET</option> + <option value="KEGG" selected="true">KEGG</option> + <option value="KO" selected="true">KO</option> + <option value="LEGIOLIST" selected="true">LEGIOLIST</option> + <option value="LEPROMA" selected="true">LEPROMA</option> + <option value="MAIZEGDB" selected="true">MAIZEGDB</option> + <option value="MALACARDS" selected="true">MALACARDS</option> + <option value="MAXQB" selected="true">MAXQB</option> + <option value="MEROPS" selected="true">MEROPS</option> + <option value="MGI" selected="true">MGI</option> + <option value="MIM" selected="true">MIM</option> + <option value="MINT" selected="true">MINT</option> + <option value="MOONPROT" selected="true">MOONPROT</option> + <option value="MYCOCLAP" selected="true">MYCOCLAP</option> + <option value="NCBI_TAXID_OH" selected="true">NCBI_TAXID_OH</option> + <option value="NCBI_TAXID_OX" selected="true">NCBI_TAXID_OX</option> + <option value="NEXTPROT" selected="true">NEXTPROT</option> + <option value="OGP" selected="true">OGP</option> + <option value="OMA" selected="true">OMA</option> + <option value="ONLINE_INFORMATION" selected="true">ONLINE_INFORMATION</option> + <option value="OPENTARGETS" selected="true">OPENTARGETS</option> + <option value="ORPHANET" selected="true">ORPHANET</option> + <option value="ORTHODB" selected="true">ORTHODB</option> + <option value="PANTHER" selected="true">PANTHER</option> + <option value="PATRIC" selected="true">PATRIC</option> + <option value="PAXDB" selected="true">PAXDB</option> + <option value="PDB" selected="true">PDB</option> + <option value="PDBSUM" selected="true">PDBSUM</option> + <option value="PEPTIDEATLAS" selected="true">PEPTIDEATLAS</option> + <option value="PEROXIBASE" selected="true">PEROXIBASE</option> + <option value="PFAM" selected="true">PFAM</option> + <option value="PHARMGKB" selected="true">PHARMGKB</option> + <option value="PHOSPHOSITEPLUS" selected="true">PHOSPHOSITEPLUS</option> + <option value="PHYLOMEDB" selected="true">PHYLOMEDB</option> + <option value="PIR" selected="true">PIR</option> + <option value="PIRNR" selected="true">PIRNR</option> + <option value="PIRSF" selected="true">PIRSF</option> + <option value="PIRSR" selected="true">PIRSR</option> + <option value="PMAP-CUTDB" selected="true">PMAP-CUTDB</option> + <option value="POMBASE" selected="true">POMBASE</option> + <option value="PRIDE" selected="true">PRIDE</option> + <option value="PRINTS" selected="true">PRINTS</option> + <option value="PRO" selected="true">PRO</option> + <option value="PRODOM" selected="true">PRODOM</option> + <option value="PROMEX" selected="true">PROMEX</option> + <option value="PROSITE" selected="true">PROSITE</option> + <option value="PROSITE-PRORULE" selected="true">PROSITE-PRORULE</option> + <option value="PROTEINMODELPORTAL" selected="true">PROTEINMODELPORTAL</option> + <option value="PROTEOMES" selected="true">PROTEOMES</option> + <option value="PSEUDOCAP" selected="true">PSEUDOCAP</option> + <option value="PUBMED" selected="true">PUBMED</option> + <option value="REACTOME" selected="true">REACTOME</option> + <option value="REBASE" selected="true">REBASE</option> + <option value="REFSEQ" selected="true">REFSEQ</option> + <option value="REPRODUCTION-2DPAGE" selected="true">REPRODUCTION-2DPAGE</option> + <option value="RGD" selected="true">RGD</option> + <option value="SABIO-RK" selected="true">SABIO-RK</option> + <option value="SGD" selected="true">SGD</option> + <option value="SIGNALINK" selected="true">SIGNALINK</option> + <option value="SIGNOR" selected="true">SIGNOR</option> + <option value="SMART" selected="true">SMART</option> + <option value="SMR" selected="true">SMR</option> + <option value="STRING" selected="true">STRING</option> + <option value="SUPFAM" selected="true">SUPFAM</option> + <option value="SWISS-2DPAGE" selected="true">SWISS-2DPAGE</option> + <option value="SWISSLIPIDS" selected="true">SWISSLIPIDS</option> + <option value="SWISSPALM" selected="true">SWISSPALM</option> + <option value="TAIR" selected="true">TAIR</option> + <option value="TCDB" selected="true">TCDB</option> + <option value="TIGRFAMS" selected="true">TIGRFAMS</option> + <option value="TOPDOWNPROTEOMICS" selected="true">TOPDOWNPROTEOMICS</option> + <option value="TREEFAM" selected="true">TREEFAM</option> + <option value="TUBERCULIST" selected="true">TUBERCULIST</option> + <option value="UCD-2DPAGE" selected="true">UCD-2DPAGE</option> + <option value="UCSC" selected="true">UCSC</option> + <option value="UNICARBKB" selected="true">UNICARBKB</option> + <option value="UNIGENE" selected="true">UNIGENE</option> + <option value="UNIPATHWAY" selected="true">UNIPATHWAY</option> + <option value="UNIPROTKB" selected="true">UNIPROTKB</option> + <option value="VECTORBASE" selected="true">VECTORBASE</option> + <option value="WBPARASITE" selected="true">WBPARASITE</option> + <option value="WORLD-2DPAGE" selected="true">WORLD-2DPAGE</option> + <option value="WORMBASE" selected="true">WORMBASE</option> + <option value="XENBASE" selected="true">XENBASE</option> + <option value="ZFIN" selected="true">ZFIN</option> + <option value="acc" selected="true">acc</option> + <option value="descAltName" selected="true">descAltName</option> + <option value="descRecName" selected="true">descRecName</option> + <option value="descSubName" selected="true">descSubName</option> + <option value="domain_source" selected="true">domain_source</option> + <option value="gene_primary_name" selected="true">gene_primary_name</option> + <option value="id" selected="true">id</option> + <option value="length" selected="true">length</option> + <option value="organism_scientific_name" selected="true">organism_scientific_name</option> + <option value="status" selected="true">status</option> + <validator type="no_options" message="Please select at least one field" /> + </param> + <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> + <param name="query_field" type="select" label="Fields" > + <option value="AGRICOLA">AGRICOLA</option> + <option value="ALLERGOME">ALLERGOME</option> + <option value="ARACHNOSERVER">ARACHNOSERVER</option> + <option value="BGEE">BGEE</option> + <option value="BINDINGDB">BINDINGDB</option> + <option value="BIOCYC">BIOCYC</option> + <option value="BIOGRID">BIOGRID</option> + <option value="BIOMUTA">BIOMUTA</option> + <option value="BRENDA">BRENDA</option> + <option value="CAZY">CAZY</option> + <option value="CCDS">CCDS</option> + <option value="CDD">CDD</option> + <option value="CGD">CGD</option> + <option value="CHEBI">CHEBI</option> + <option value="CHEMBL">CHEMBL</option> + <option value="CHITARS">CHITARS</option> + <option value="CLEANEX">CLEANEX</option> + <option value="CODING">CODING</option> + <option value="COLLECTF">COLLECTF</option> + <option value="COMPLUYEAST-2DPAGE">COMPLUYEAST-2DPAGE</option> + <option value="CONOSERVER">CONOSERVER</option> + <option value="CTD">CTD</option> + <option value="DEPOD">DEPOD</option> + <option value="DI">DI</option> + <option value="DICTYBASE">DICTYBASE</option> + <option value="DIP">DIP</option> + <option value="DISGENET">DISGENET</option> + <option value="DISPROT">DISPROT</option> + <option value="DMDM">DMDM</option> + <option value="DNASU">DNASU</option> + <option value="DOI">DOI</option> + <option value="DOSAC-COBS-2DPAGE">DOSAC-COBS-2DPAGE</option> + <option value="DRUGBANK">DRUGBANK</option> + <option value="EC">EC</option> + <option value="ECHOBASE">ECHOBASE</option> + <option value="ECNUMBER">ECNUMBER</option> + <option value="ECOGENE">ECOGENE</option> + <option value="EGGNOG">EGGNOG</option> + <option value="EMBL">EMBL</option> + <option value="ENSEMBL">ENSEMBL</option> + <option value="ENSEMBLBACTERIA">ENSEMBLBACTERIA</option> + <option value="ENSEMBLFUNGI">ENSEMBLFUNGI</option> + <option value="ENSEMBLMETAZOA">ENSEMBLMETAZOA</option> + <option value="ENSEMBLPLANTS">ENSEMBLPLANTS</option> + <option value="ENSEMBLPROTISTS">ENSEMBLPROTISTS</option> + <option value="ENSEMBL_GENE">ENSEMBL_GENE</option> + <option value="ENSEMBL_PROTEIN">ENSEMBL_PROTEIN</option> + <option value="ENSEMBL_TRANSCRIPT">ENSEMBL_TRANSCRIPT</option> + <option value="EPD">EPD</option> + <option value="ESTHER">ESTHER</option> + <option value="EUHCVDB">EUHCVDB</option> + <option value="EUPATHDB">EUPATHDB</option> + <option value="EVOLUTIONARYTRACE">EVOLUTIONARYTRACE</option> + <option value="EXPRESSIONATLAS">EXPRESSIONATLAS</option> + <option value="FLYBASE">FLYBASE</option> + <option value="GENE3D">GENE3D</option> + <option value="GENECARDS">GENECARDS</option> + <option value="GENEDB">GENEDB</option> + <option value="GENEID">GENEID</option> + <option value="GENEREVIEWS">GENEREVIEWS</option> + <option value="GENETREE">GENETREE</option> + <option value="GENEVISIBLE">GENEVISIBLE</option> + <option value="GENEWIKI">GENEWIKI</option> + <option value="GENOMERNAI">GENOMERNAI</option> + <option value="GO">GO</option> + <option value="GRAMENE">GRAMENE</option> + <option value="GUIDETOPHARMACOLOGY">GUIDETOPHARMACOLOGY</option> + <option value="H-INVDB">H-INVDB</option> + <option value="HAMAP">HAMAP</option> + <option value="HAMAP-RULE">HAMAP-RULE</option> + <option value="HGNC">HGNC</option> + <option value="HOGENOM">HOGENOM</option> + <option value="HOVERGEN">HOVERGEN</option> + <option value="HPA">HPA</option> + <option value="INPARANOID">INPARANOID</option> + <option value="INTACT">INTACT</option> + <option value="INTERPRO">INTERPRO</option> + <option value="IPTMNET">IPTMNET</option> + <option value="KEGG">KEGG</option> + <option value="KO">KO</option> + <option value="LEGIOLIST">LEGIOLIST</option> + <option value="LEPROMA">LEPROMA</option> + <option value="MAIZEGDB">MAIZEGDB</option> + <option value="MALACARDS">MALACARDS</option> + <option value="MAXQB">MAXQB</option> + <option value="MEROPS">MEROPS</option> + <option value="MGI">MGI</option> + <option value="MIM">MIM</option> + <option value="MINT">MINT</option> + <option value="MOONPROT">MOONPROT</option> + <option value="MYCOCLAP">MYCOCLAP</option> + <option value="NCBI_TAXID_OH">NCBI_TAXID_OH</option> + <option value="NCBI_TAXID_OX">NCBI_TAXID_OX</option> + <option value="NEXTPROT">NEXTPROT</option> + <option value="OGP">OGP</option> + <option value="OMA">OMA</option> + <option value="ONLINE_INFORMATION">ONLINE_INFORMATION</option> + <option value="OPENTARGETS">OPENTARGETS</option> + <option value="ORPHANET">ORPHANET</option> + <option value="ORTHODB">ORTHODB</option> + <option value="PANTHER">PANTHER</option> + <option value="PATRIC">PATRIC</option> + <option value="PAXDB">PAXDB</option> + <option value="PDB">PDB</option> + <option value="PDBSUM">PDBSUM</option> + <option value="PEPTIDEATLAS">PEPTIDEATLAS</option> + <option value="PEROXIBASE">PEROXIBASE</option> + <option value="PFAM">PFAM</option> + <option value="PHARMGKB">PHARMGKB</option> + <option value="PHOSPHOSITEPLUS">PHOSPHOSITEPLUS</option> + <option value="PHYLOMEDB">PHYLOMEDB</option> + <option value="PIR">PIR</option> + <option value="PIRNR">PIRNR</option> + <option value="PIRSF">PIRSF</option> + <option value="PIRSR">PIRSR</option> + <option value="PMAP-CUTDB">PMAP-CUTDB</option> + <option value="POMBASE">POMBASE</option> + <option value="PRIDE">PRIDE</option> + <option value="PRINTS">PRINTS</option> + <option value="PRO">PRO</option> + <option value="PRODOM">PRODOM</option> + <option value="PROMEX">PROMEX</option> + <option value="PROSITE">PROSITE</option> + <option value="PROSITE-PRORULE">PROSITE-PRORULE</option> + <option value="PROTEINMODELPORTAL">PROTEINMODELPORTAL</option> + <option value="PROTEOMES">PROTEOMES</option> + <option value="PSEUDOCAP">PSEUDOCAP</option> + <option value="PUBMED">PUBMED</option> + <option value="REACTOME">REACTOME</option> + <option value="REBASE">REBASE</option> + <option value="REFSEQ">REFSEQ</option> + <option value="REPRODUCTION-2DPAGE">REPRODUCTION-2DPAGE</option> + <option value="RGD">RGD</option> + <option value="RULEBASE">RULEBASE</option> + <option value="SAAS">SAAS</option> + <option value="SABIO-RK">SABIO-RK</option> + <option value="SAM">SAM</option> + <option value="SGD">SGD</option> + <option value="SIGNALINK">SIGNALINK</option> + <option value="SIGNOR">SIGNOR</option> + <option value="SMART">SMART</option> + <option value="SMR">SMR</option> + <option value="STRING">STRING</option> + <option value="SUPFAM">SUPFAM</option> + <option value="SWISS-2DPAGE">SWISS-2DPAGE</option> + <option value="SWISSLIPIDS">SWISSLIPIDS</option> + <option value="SWISSPALM">SWISSPALM</option> + <option value="TAIR">TAIR</option> + <option value="TCDB">TCDB</option> + <option value="TIGRFAMS">TIGRFAMS</option> + <option value="TOPDOWNPROTEOMICS">TOPDOWNPROTEOMICS</option> + <option value="TREEFAM">TREEFAM</option> + <option value="TUBERCULIST">TUBERCULIST</option> + <option value="UCD-2DPAGE">UCD-2DPAGE</option> + <option value="UCSC">UCSC</option> + <option value="UNICARBKB">UNICARBKB</option> + <option value="UNIGENE">UNIGENE</option> + <option value="UNIPATHWAY">UNIPATHWAY</option> + <option value="UNIPROTKB">UNIPROTKB</option> + <option value="VECTORBASE">VECTORBASE</option> + <option value="WBPARASITE">WBPARASITE</option> + <option value="WORLD-2DPAGE">WORLD-2DPAGE</option> + <option value="WORMBASE">WORMBASE</option> + <option value="XENBASE">XENBASE</option> + <option value="ZFIN">ZFIN</option> + <option value="acc">acc</option> + <option value="chromosome">chromosome</option> + <option value="crc64_iso">crc64_iso</option> + <option value="creation_date">creation_date</option> + <option value="descRecName">descRecName</option> + <option value="description">description</option> + <option value="disease_name">disease_name</option> + <option value="domain_source">domain_source</option> + <option value="gene_ORF_name">gene_ORF_name</option> + <option value="gene_ordered_locus_name">gene_ordered_locus_name</option> + <option value="gene_primary_name">gene_primary_name</option> + <option value="gene_synonym_name">gene_synonym_name</option> + <option value="id">id</option> + <option value="keyword_id">keyword_id</option> + <option value="keywords">keywords</option> + <option value="last_modification_date">last_modification_date</option> + <option value="length">length</option> + <option value="md5">md5</option> + <option value="organelle">organelle</option> + <option value="organism_classification">organism_classification</option> + <option value="organism_host_species">organism_host_species</option> + <option value="organism_scientific_name">organism_scientific_name</option> + <option value="organism_species">organism_species</option> + <option value="protein_existence">protein_existence</option> + <option value="references">references</option> + <option value="sequence_fragment">sequence_fragment</option> + <option value="sequence_last_modif_date">sequence_last_modif_date</option> + <option value="status">status</option> + </param> + <conditional name="comp_operation"> + <param name="operation" type="select" label="Comparison operation" > + <option value="equal">equal</option> + <option value="not">not</option> + <option value="range">range</option> + </param> + <when value="equal"> + <param name="query_text" type="text" label="Searched term"/> + </when> + <when value="not"> + <param name="query_text" type="text" label="Searched term"/> + <param name="not_query_text" type="text" label="Limiting term"/> + </when> + <when value="range"> + <param name="min" type="text" label="From"/> + <param name="max" type="text" label="To"/> + </when> + </conditional> + </repeat> + </when> + + <when value="uniref100"> + <param name="fields" type="select" label="Fields to extract" multiple="true"> + <option value="TAXONOMY" selected="true">TAXONOMY</option> + <option value="UNIPARC" selected="true">UNIPARC</option> + <option value="UNIPROT" selected="true">UNIPROT</option> + <option value="UNIREF50" selected="true">UNIREF50</option> + <option value="UNIREF90" selected="true">UNIREF90</option> + <option value="domain_source" selected="true">domain_source</option> + <option value="id" selected="true">id</option> + <option value="length" selected="true">length</option> + <option value="name" selected="true">name</option> + <validator type="no_options" message="Please select at least one field" /> + </param> + <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> + <param name="query_field" type="select" label="Fields" > + <option value="TAXONOMY">TAXONOMY</option> + <option value="UNIPARC">UNIPARC</option> + <option value="UNIPROT">UNIPROT</option> + <option value="UNIREF50">UNIREF50</option> + <option value="UNIREF90">UNIREF90</option> + <option value="crc64_iso">crc64_iso</option> + <option value="dbref_protein_name">dbref_protein_name</option> + <option value="dbref_source_organism">dbref_source_organism</option> + <option value="dbref_uniprotkb_id">dbref_uniprotkb_id</option> + <option value="domain_source">domain_source</option> + <option value="entry_common_taxon">entry_common_taxon</option> + <option value="entry_common_taxon_id">entry_common_taxon_id</option> + <option value="id">id</option> + <option value="last_modification_date">last_modification_date</option> + <option value="length">length</option> + <option value="md5">md5</option> + <option value="name">name</option> + </param> + <conditional name="comp_operation"> + <param name="operation" type="select" label="Comparison operation" > + <option value="equal">equal</option> + <option value="not">not</option> + <option value="range">range</option> + </param> + <when value="equal"> + <param name="query_text" type="text" label="Searched term"/> + </when> + <when value="not"> + <param name="query_text" type="text" label="Searched term"/> + <param name="not_query_text" type="text" label="Limiting term"/> + </when> + <when value="range"> + <param name="min" type="text" label="From"/> + <param name="max" type="text" label="To"/> + </when> + </conditional> + </repeat> + </when> + + <when value="uniref50"> + <param name="fields" type="select" label="Fields to extract" multiple="true"> + <option value="TAXONOMY" selected="true">TAXONOMY</option> + <option value="UNIPARC" selected="true">UNIPARC</option> + <option value="UNIPROT" selected="true">UNIPROT</option> + <option value="UNIREF100" selected="true">UNIREF100</option> + <option value="UNIREF90" selected="true">UNIREF90</option> + <option value="domain_source" selected="true">domain_source</option> + <option value="id" selected="true">id</option> + <option value="length" selected="true">length</option> + <option value="name" selected="true">name</option> + <validator type="no_options" message="Please select at least one field" /> + </param> + <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> + <param name="query_field" type="select" label="Fields" > + <option value="TAXONOMY">TAXONOMY</option> + <option value="UNIPARC">UNIPARC</option> + <option value="UNIPROT">UNIPROT</option> + <option value="UNIREF100">UNIREF100</option> + <option value="UNIREF90">UNIREF90</option> + <option value="crc64_iso">crc64_iso</option> + <option value="dbref_protein_name">dbref_protein_name</option> + <option value="dbref_source_organism">dbref_source_organism</option> + <option value="dbref_uniprotkb_id">dbref_uniprotkb_id</option> + <option value="domain_source">domain_source</option> + <option value="entry_common_taxon">entry_common_taxon</option> + <option value="entry_common_taxon_id">entry_common_taxon_id</option> + <option value="id">id</option> + <option value="last_modification_date">last_modification_date</option> + <option value="length">length</option> + <option value="md5">md5</option> + <option value="name">name</option> + </param> + <conditional name="comp_operation"> + <param name="operation" type="select" label="Comparison operation" > + <option value="equal">equal</option> + <option value="not">not</option> + <option value="range">range</option> + </param> + <when value="equal"> + <param name="query_text" type="text" label="Searched term"/> + </when> + <when value="not"> + <param name="query_text" type="text" label="Searched term"/> + <param name="not_query_text" type="text" label="Limiting term"/> + </when> + <when value="range"> + <param name="min" type="text" label="From"/> + <param name="max" type="text" label="To"/> + </when> + </conditional> + </repeat> + </when> + + <when value="uniref90"> + <param name="fields" type="select" label="Fields to extract" multiple="true"> + <option value="TAXONOMY" selected="true">TAXONOMY</option> + <option value="UNIPARC" selected="true">UNIPARC</option> + <option value="UNIPROT" selected="true">UNIPROT</option> + <option value="UNIREF100" selected="true">UNIREF100</option> + <option value="UNIREF50" selected="true">UNIREF50</option> + <option value="domain_source" selected="true">domain_source</option> + <option value="id" selected="true">id</option> + <option value="length" selected="true">length</option> + <option value="name" selected="true">name</option> + <validator type="no_options" message="Please select at least one field" /> + </param> + <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> + <param name="query_field" type="select" label="Fields" > + <option value="TAXONOMY">TAXONOMY</option> + <option value="UNIPARC">UNIPARC</option> + <option value="UNIPROT">UNIPROT</option> + <option value="UNIREF100">UNIREF100</option> + <option value="UNIREF50">UNIREF50</option> + <option value="crc64_iso">crc64_iso</option> + <option value="dbref_protein_name">dbref_protein_name</option> + <option value="dbref_source_organism">dbref_source_organism</option> + <option value="dbref_uniprotkb_id">dbref_uniprotkb_id</option> + <option value="domain_source">domain_source</option> + <option value="entry_common_taxon">entry_common_taxon</option> + <option value="entry_common_taxon_id">entry_common_taxon_id</option> + <option value="id">id</option> + <option value="last_modification_date">last_modification_date</option> + <option value="length">length</option> + <option value="md5">md5</option> + <option value="name">name</option> + </param> + <conditional name="comp_operation"> + <param name="operation" type="select" label="Comparison operation" > + <option value="equal">equal</option> + <option value="not">not</option> + <option value="range">range</option> + </param> + <when value="equal"> + <param name="query_text" type="text" label="Searched term"/> + </when> + <when value="not"> + <param name="query_text" type="text" label="Searched term"/> + <param name="not_query_text" type="text" label="Limiting term"/> + </when> + <when value="range"> + <param name="min" type="text" label="From"/> + <param name="max" type="text" label="To"/> + </when> + </conditional> + </repeat> + </when> + + <when value="wormbaseParasite"> + <param name="fields" type="select" label="Fields to extract" multiple="true"> + <option value="ARRAYEXPRESS" selected="true">ARRAYEXPRESS</option> + <option value="EMBL" selected="true">EMBL</option> + <option value="ENSEMBL_ORTHOLOG" selected="true">ENSEMBL_ORTHOLOG</option> + <option value="ENTREZGENE" selected="true">ENTREZGENE</option> + <option value="EPD" selected="true">EPD</option> + <option value="GENEDB" selected="true">GENEDB</option> + <option value="GO" selected="true">GO</option> + <option value="INTERPRO" selected="true">INTERPRO</option> + <option value="KEGG_ENZYME" selected="true">KEGG_ENZYME</option> + <option value="MEROPS" selected="true">MEROPS</option> + <option value="METACYC" selected="true">METACYC</option> + <option value="NCBI_TAXONOMY_ID" selected="true">NCBI_TAXONOMY_ID</option> + <option value="PDB" selected="true">PDB</option> + <option value="PROTEIN_ID" selected="true">PROTEIN_ID</option> + <option value="REACTOME" selected="true">REACTOME</option> + <option value="REFSEQ_MRNA" selected="true">REFSEQ_MRNA</option> + <option value="REFSEQ_MRNA_PREDICTED" selected="true">REFSEQ_MRNA_PREDICTED</option> + <option value="REFSEQ_NCRNA" selected="true">REFSEQ_NCRNA</option> + <option value="REFSEQ_PEPTIDE" selected="true">REFSEQ_PEPTIDE</option> + <option value="REFSEQ_PEPTIDE_PREDICTED" selected="true">REFSEQ_PEPTIDE_PREDICTED</option> + <option value="SCHISTODB" selected="true">SCHISTODB</option> + <option value="UNIGENE" selected="true">UNIGENE</option> + <option value="UNIPARC" selected="true">UNIPARC</option> + <option value="UNIPATHWAY" selected="true">UNIPATHWAY</option> + <option value="UNIPROT" selected="true">UNIPROT</option> + <option value="WIKIGENE" selected="true">WIKIGENE</option> + <option value="WORMBASE_GENE" selected="true">WORMBASE_GENE</option> + <option value="WORMBASE_GSEQNAME" selected="true">WORMBASE_GSEQNAME</option> + <option value="WORMBASE_LOCUS" selected="true">WORMBASE_LOCUS</option> + <option value="WORMBASE_TRANSCRIPT" selected="true">WORMBASE_TRANSCRIPT</option> + <option value="WORMPEP_ID" selected="true">WORMPEP_ID</option> + <option value="description" selected="true">description</option> + <option value="domain_source" selected="true">domain_source</option> + <option value="exon" selected="true">exon</option> + <option value="exon_count" selected="true">exon_count</option> + <option value="featuretype" selected="true">featuretype</option> + <option value="gene_name" selected="true">gene_name</option> + <option value="gene_synonym" selected="true">gene_synonym</option> + <option value="genetree" selected="true">genetree</option> + <option value="genomic_unit" selected="true">genomic_unit</option> + <option value="id" selected="true">id</option> + <option value="location" selected="true">location</option> + <option value="name" selected="true">name</option> + <option value="peptide" selected="true">peptide</option> + <option value="source" selected="true">source</option> + <option value="species" selected="true">species</option> + <option value="system_name" selected="true">system_name</option> + <option value="transcript" selected="true">transcript</option> + <option value="transcript_count" selected="true">transcript_count</option> + <validator type="no_options" message="Please select at least one field" /> + </param> + <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> + <param name="query_field" type="select" label="Fields" > + <option value="ARRAYEXPRESS">ARRAYEXPRESS</option> + <option value="EMBL">EMBL</option> + <option value="ENSEMBL_ORTHOLOG">ENSEMBL_ORTHOLOG</option> + <option value="ENTREZGENE">ENTREZGENE</option> + <option value="EPD">EPD</option> + <option value="GENEDB">GENEDB</option> + <option value="GO">GO</option> + <option value="INTERPRO">INTERPRO</option> + <option value="KEGG_ENZYME">KEGG_ENZYME</option> + <option value="MEROPS">MEROPS</option> + <option value="METACYC">METACYC</option> + <option value="NCBI_TAXONOMY_ID">NCBI_TAXONOMY_ID</option> + <option value="PDB">PDB</option> + <option value="PROTEIN_ID">PROTEIN_ID</option> + <option value="REACTOME">REACTOME</option> + <option value="REFSEQ_MRNA">REFSEQ_MRNA</option> + <option value="REFSEQ_MRNA_PREDICTED">REFSEQ_MRNA_PREDICTED</option> + <option value="REFSEQ_NCRNA">REFSEQ_NCRNA</option> + <option value="REFSEQ_PEPTIDE">REFSEQ_PEPTIDE</option> + <option value="REFSEQ_PEPTIDE_PREDICTED">REFSEQ_PEPTIDE_PREDICTED</option> + <option value="SCHISTODB">SCHISTODB</option> + <option value="UNIGENE">UNIGENE</option> + <option value="UNIPARC">UNIPARC</option> + <option value="UNIPATHWAY">UNIPATHWAY</option> + <option value="UNIPROT">UNIPROT</option> + <option value="WIKIGENE">WIKIGENE</option> + <option value="WORMBASE_GENE">WORMBASE_GENE</option> + <option value="WORMBASE_GSEQNAME">WORMBASE_GSEQNAME</option> + <option value="WORMBASE_LOCUS">WORMBASE_LOCUS</option> + <option value="WORMBASE_TRANSCRIPT">WORMBASE_TRANSCRIPT</option> + <option value="WORMPEP_ID">WORMPEP_ID</option> + <option value="collection">collection</option> + <option value="database">database</option> + <option value="description">description</option> + <option value="domain">domain</option> + <option value="domain_count">domain_count</option> + <option value="domain_source">domain_source</option> + <option value="exon">exon</option> + <option value="gene_name">gene_name</option> + <option value="gene_synonym">gene_synonym</option> + <option value="genetree">genetree</option> + <option value="genomic_unit">genomic_unit</option> + <option value="haplotype">haplotype</option> + <option value="id">id</option> + <option value="id_noversion">id_noversion</option> + <option value="name">name</option> + <option value="peptide">peptide</option> + <option value="seq_region_name">seq_region_name</option> + <option value="source">source</option> + <option value="species">species</option> + <option value="system_name">system_name</option> + <option value="transcript">transcript</option> + </param> + <conditional name="comp_operation"> + <param name="operation" type="select" label="Comparison operation" > + <option value="equal">equal</option> + <option value="not">not</option> + <option value="range">range</option> + </param> + <when value="equal"> + <param name="query_text" type="text" label="Searched term"/> + </when> + <when value="not"> + <param name="query_text" type="text" label="Searched term"/> + <param name="not_query_text" type="text" label="Limiting term"/> + </when> + <when value="range"> + <param name="min" type="text" label="From"/> + <param name="max" type="text" label="To"/> + </when> + </conditional> + </repeat> + </when> + + </conditional> + </xml> + <xml name="citations"> + <citations> + <citation type="doi">10.1093/bib/bbp065</citation> + <citation type="doi">10.1093/nar/gkv316</citation> + </citations> + </xml> +</macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ERR675640_qc-stats_stats Thu Dec 01 15:27:59 2016 -0500 @@ -0,0 +1,13 @@ +bp_count 85213813 +sequence_count 670470 +average_length 127.096 +standard_deviation_length 17.309 +length_min 100 +length_max 159 +average_gc_content 49.226 +standard_deviation_gc_content 9.333 +average_gc_ratio 1.117 +standard_deviation_gc_ratio 0.470 +ambig_char_count 6 +ambig_sequence_count 6 +average_ambig_chars 0.000