Mercurial > repos > bgruening > uniprot_rest_interface
changeset 9:468c71dac78a draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit da476148d1c609f5c26e880a3e593f0fa71ff2f6
| author | bgruening |
|---|---|
| date | Wed, 22 May 2024 21:18:15 +0000 |
| parents | af5eccf83605 |
| children | 95fb5712344f |
| files | macros.xml test-data/test2_map.tab uniprot.py uniprot.xml |
| diffstat | 4 files changed, 1048 insertions(+), 473 deletions(-) [+] |
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--- a/macros.xml Mon Nov 21 22:02:41 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,226 +0,0 @@ -<macros> -<token name="@EXECUTABLE@">1.0</token> - <macro name="macro-category_FROM"> - <param name="category_FROM" type="select" label="Choose your database category (FROM):" - help="Select a databse from which your ids are coming from"> - <option value="uniprot">UniProt</option> - <option value="oseqdb">Other sequence databases</option> - <option value="3Dstrdb">3D structure databases</option> - <option value="ppidb">Protein-protein interaction databases</option> - <option value="chemistry">Chemistry</option> - <option value="protfgdb">Protein family/group databases</option> - <option value="polymorphismANDmutation">Polymorphism and mutation databases</option> - <option value="2DgelDB">2D gel databases</option> - <option value="ProtocolsMaterialsDB">Protocols and materials databases</option> - <option value="GenomeAnnotationDB">Genome annotation databases</option> - <option value="OrganismSpecificGeneDB">Organism-specific gene databases</option> - <option value="phylogenomic">Phylogenomic databases</option> - <option value="EnzymePathwayDB">Enzyme and pathway databases</option> - <option value="GeneExpression">Gene expression databases</option> - <option value="other">Other</option> - </param> - </macro> - <macro name="macro-category_TO"> - <param name="category_TO" type="select" label="Choose your database category (TO):" - help="Select a database which will be used for mapping"> - <option value="uniprot">UniProt</option> - <option value="oseqdb">Other sequence databases</option> - <option value="3Dstrdb">3D structure databases</option> - <option value="ppidb">Protein-protein interaction databases</option> - <option value="chemistry">Chemistry</option> - <option value="protfgdb">Protein family/group databases</option> - <option value="polymorphismANDmutation">Polymorphism and mutation databases</option> - <option value="2DgelDB">2D gel databases</option> - <option value="ProtocolsMaterialsDB">Protocols and materials databases</option> - <option value="GenomeAnnotationDB">Genome annotation databases</option> - <option value="OrganismSpecificGeneDB">Organism-specific gene databases</option> - <option value="phylogenomic">Phylogenomic databases</option> - <option value="EnzymePathwayDB">Enzyme and pathway databases</option> - <option value="GeneExpression">Gene expression databases</option> - <option value="other">Other</option> - </param> - </macro> - <macro name="macro-db_uniprot_FROM"> - <param name="db_uniprot_FROM" type="select" label="Choose a database:" - help=""> - <option value="ACC+ID">UniProtKB AC/ID</option> - <option value="ACC">UniProtKB AC</option> - <option value="ID">UniProtKB ID</option> - <option value="UPARC">UniParc</option> - <option value="NF50">UniRef50</option> - <option value="NF90">UniRef90</option> - <option value="NF100">UniRef100</option> - <option value="GENENAME">Gene name</option> - </param> - </macro> - <macro name="macro-db_uniprot_TO"> - <param name="db_uniprot_TO" type="select" label="Choose a database:" - help=""> - <option value="ACC">UniProtKB AC</option> - <option value="ID">UniProtKB ID</option> - <option value="UPARC">UniParc</option> - <option value="NF50">UniRef50</option> - <option value="NF90">UniRef90</option> - <option value="NF100">UniRef100</option> - <option value="GENENAME">Gene name</option> - </param> - </macro> - <macro name="macro-db_oseqdb"> - <param name="db_oseqdb" type="select" label="Choose a database:" - help=""> - <option value="EMBL_ID">EMBL/GenBank/DDBJ</option> - <option value="EMBL">EMBL/GenBank/DDBJ CDS</option> - <option value="PIR">PIR</option> - - <option value="UNIGENE_ID">UniParc</option> - <option value="P_ENTREZGENEID">Entrez Gene (GeneID)</option> - <option value="P_GI">GI number</option> - <option value="P_REFSEQ_AC">RefSeq Protein</option> - <option value="REFSEQ_NT_ID">RefSeq Nucleotide</option> - </param> - </macro> - <macro name="macro-db_3Dstrdb"> - <param name="db_3Dstrdb" type="select" label="Choose a database:" - help=""> - <option value="PDB_ID">PDB</option> - <option value="DISPROT_ID">DisProt</option> - </param> - </macro> - <macro name="macro-db_ppidb"> - <param name="db_ppidb" type="select" label="Choose a database:" - help=""> - <option value="BIOGRID_ID">BioGrid</option> - <option value="DIP_ID">DIP</option> - <option value="MINT_ID">MINT</option> - <option value="STRING_ID">STRING</option> - </param> - </macro> - <macro name="macro-db_chemistry"> - <param name="db_chemistry" type="select" label="Choose a database:" - help=""> - <option value="CHEMBL_ID">ChEMBL</option> - <option value="DrugBank_ID">DrugBank</option> - <option value="GUIDETOPHARMACOLOGY_ID">GuidetoPHARMACOLOGY</option> - </param> - </macro> - <macro name="macro-db_protfgdb"> - <param name="db_protfgdb" type="select" label="Choose a database:" - help=""> - <option value="ALLERGOME_ID">Allergome</option> - <option value="MEROPS_ID">MEROPS</option> - <option value="MYCOCLAP_ID">mycoCLAP</option> - <option value="PEROXIBASE_ID">PeroxiBase</option> - <option value="REBASE_ID">REBASE</option> - <option value="TCDB_ID">TCDB</option> - </param> - </macro> - <macro name="macro-db_polymorphismANDmutation"> - <param name="db_polymorphismANDmutation" type="select" label="Choose a database:" - help=""> - <option value="DMDM_ID">DMDM</option> - </param> - </macro> - <macro name="macro-db_2DgelDB"> - <param name="db_2DgelDB" type="select" label="Choose a database:" - help=""> - <option value="WORLD_2DPAGE_ID">World-2DPAGE</option> - </param> - </macro> - <macro name="macro-db_ProtocolsMaterialsDB"> - <param name="db_ProtocolsMaterialsDB" type="select" label="Choose a database:" - help=""> - <option value="DNASU_ID">DNASU</option> - </param> - </macro> - <macro name="macro-db_GenomeAnnotationDB"> - <param name="db_GenomeAnnotationDB" type="select" label="Choose a database:" - help=""> - <option value="ENSEMBL_ID">Ensembl</option> - <option value="ENSEMBL_PRO_ID">Ensembl Protein</option> - <option value="ENSEMBL_TRS_ID">Ensembl Transcript</option> - <option value="ENSEMBLGENOME_ID">Ensembl Genomes</option> - <option value="ENSEMBLGENOME_PRO_ID">Ensembl Genomes Protein</option> - <option value="ENSEMBLGENOME_TRS_ID">Ensembl Genomes Transcript</option> - <option value="P_ENTREZGENEID">GeneID</option> - <option value="KEGG_ID">KEGG</option> - <option value="PATRIC_ID">PATRIC</option> - <option value="UCSC_ID">UCSC</option> - <option value="VECTORBASE_ID">VectorBase</option> - </param> - </macro> - <macro name="macro-db_OrganismSpecificGeneDB"> - <param name="db_OrganismSpecificGeneDB" type="select" label="Choose a database:" - help=""> - <option value="ARACHNOSERVER_ID">ArachnoServer</option> - <option value="CGD">CGD</option> - <option value="CONOSERVER_ID">ConoServer</option> - <option value="DICTYBASE_ID">dictyBase</option> - <option value="ECHOBASE_ID">EchoBASE</option> - <option value="ECOGENE_ID">EcoGene</option> - <option value="EUHCVDB_ID">euHCVdb</option> - <option value="EUPATHDB_ID">EuPathDB</option> - <option value="FLYBASE_ID">FlyBase</option> - <option value="GENECARDS_ID">GeneCards</option> - <option value="GENEFARM_ID">GeneFarm</option> - <option value="GENOLIST_ID">GenoList</option> - <option value="H_INVDB_ID">H-InvDB</option> - <option value="HGNC_ID">HGNC</option> - <option value="HPA_ID">HPA</option> - <option value="LEGIOLIST_ID">LegioList</option> - <option value="MAIZEGDB_ID">MaizeGDB</option> - <option value="MIM_ID">MIM</option> - <option value="MGI_ID">MGI</option> - <option value="NEXTPROT_ID">neXtProt</option> - <option value="ORPHANET_ID">Orphanet</option> - <option value="PHARMGKB_ID">PharmGKB</option> - <option value="POMBASE_ID">PomBase</option> - <option value="PSEUDOCAP_ID">PseudoCAP</option> - <option value="RGD_ID">RGD</option> - <option value="SGD_ID">SGD</option> - <option value="TAIR_ID">TAIR</option> - <option value="TUBERCULIST_ID">TubercuList</option> - <option value="WORMBASE_ID">WormBase</option> - <option value="WORMBASE_TRS_ID">WormBase Transcript</option> - <option value="WORMBASE_PRO_ID">WormBase Protein</option> - <option value="XENBASE_ID">Xenbase</option> - <option value="ZFIN_ID">ZFIN</option> - </param> - </macro> - <macro name="macro-db_phylogenomic"> - <param name="db_phylogenomic" type="select" label="Choose a database:" - help=""> - <option value="EGGNOG_ID">eggNOG</option> - <option value="GENETREE_ID">GeneTree</option> - <option value="HOGENOM_ID">HOGENOM</option> - <option value="HOVERGEN_ID">HOVERGEN</option> - <option value="KO_ID">KO</option> - <option value="OMA_ID">OMA</option> - <option value="ORTHODB_ID">OrthoDB</option> - <option value="PROTCLUSTDB_ID">ProtClustDB</option> - <option value="TREEFAM_ID">TreeFam</option> - </param> - </macro> - <macro name="macro-db_EnzymePathwayDB"> - <param name="db_EnzymePathwayDB" type="select" label="Choose a database:" - help=""> - <option value="BIOCYC_ID">BioCyc</option> - <option value="REACTOME_ID">Reactome</option> - <option value="UNIPATHWAY_ID">UniPathWay</option> - </param> - </macro> - <macro name="macro-db_GeneExpression"> - <param name="db_GeneExpression" type="select" label="Choose a database:" - help=""> - <option value="CLEANEX_ID">CleanEx</option> - </param> - </macro> - <macro name="macro-db_other"> - <param name="db_other" type="select" label="Choose a database:" - help=""> - <option value="CHITARS_ID">ChiTaRS</option> - <option value="GENOMERNAI_ID">GenomeRNAi</option> - <option value="GENEWIKI_ID">GeneWiki</option> - <option value="NEXTBIO_ID">NextBio</option> - </param> - </macro> -</macros>
--- a/test-data/test2_map.tab Mon Nov 21 22:02:41 2022 +0000 +++ b/test-data/test2_map.tab Wed May 22 21:18:15 2024 +0000 @@ -1,4 +1,4 @@ -From To -NM_001087 AAMP_HUMAN -NM_130786 A1BG_HUMAN -NM_130786 V9HWD8_HUMAN +From Entry Entry Name Reviewed Protein names Gene Names Organism Length +NM_001087 Q13685 AAMP_HUMAN reviewed Angio-associated migratory cell protein AAMP Homo sapiens (Human) 434 +NM_130786 P04217 A1BG_HUMAN reviewed Alpha-1B-glycoprotein (Alpha-1-B glycoprotein) A1BG Homo sapiens (Human) 495 +NM_130786 V9HWD8 V9HWD8_HUMAN unreviewed Epididymis secretory sperm binding protein Li 163pA HEL-S-163pA Homo sapiens (Human) 495
--- a/uniprot.py Mon Nov 21 22:02:41 2022 +0000 +++ b/uniprot.py Wed May 22 21:18:15 2024 +0000 @@ -1,92 +1,266 @@ -#!/usr/bin/env python -""" -uniprot python interface -to access the uniprot database - -Based on work from Jan Rudolph: https://github.com/jdrudolph/uniprot -available services: - map - retrieve - -rewitten using inspiration form: https://findwork.dev/blog/advanced-usage-python-requests-timeouts-retries-hooks/ -""" import argparse +import json +import re import sys +import time +import zlib +from urllib.parse import ( + parse_qs, + urlencode, + urlparse, +) +from xml.etree import ElementTree import requests -from requests.adapters import HTTPAdapter -from requests.packages.urllib3.util.retry import Retry - - -DEFAULT_TIMEOUT = 5 # seconds -URL = 'https://legacy.uniprot.org/' - -retry_strategy = Retry( - total=5, - backoff_factor=2, - status_forcelist=[429, 500, 502, 503, 504], - allowed_methods=["HEAD", "GET", "OPTIONS", "POST"] +from requests.adapters import ( + HTTPAdapter, + Retry, ) -class TimeoutHTTPAdapter(HTTPAdapter): - def __init__(self, *args, **kwargs): - self.timeout = DEFAULT_TIMEOUT - if "timeout" in kwargs: - self.timeout = kwargs["timeout"] - del kwargs["timeout"] - super().__init__(*args, **kwargs) +POLLING_INTERVAL = 3 +API_URL = "https://rest.uniprot.org" + + +retries = Retry(total=5, backoff_factor=0.25, status_forcelist=[500, 502, 503, 504]) +session = requests.Session() +session.mount("https://", HTTPAdapter(max_retries=retries)) + + +def check_response(response): + try: + response.raise_for_status() + except requests.HTTPError: + print(response.json()) + raise + + +def submit_id_mapping(from_db, to_db, ids): + print(f"{from_db} {to_db}") + request = requests.post( + f"{API_URL}/idmapping/run", + data={"from": from_db, "to": to_db, "ids": ",".join(ids)}, + ) + check_response(request) + return request.json()["jobId"] + + +def get_next_link(headers): + re_next_link = re.compile(r'<(.+)>; rel="next"') + if "Link" in headers: + match = re_next_link.match(headers["Link"]) + if match: + return match.group(1) + + +def check_id_mapping_results_ready(job_id): + while True: + request = session.get(f"{API_URL}/idmapping/status/{job_id}") + check_response(request) + j = request.json() + if "jobStatus" in j: + if j["jobStatus"] == "RUNNING": + print(f"Retrying in {POLLING_INTERVAL}s") + time.sleep(POLLING_INTERVAL) + else: + raise Exception(j["jobStatus"]) + else: + return bool(j["results"] or j["failedIds"]) + + +def get_batch(batch_response, file_format, compressed): + batch_url = get_next_link(batch_response.headers) + while batch_url: + batch_response = session.get(batch_url) + batch_response.raise_for_status() + yield decode_results(batch_response, file_format, compressed) + batch_url = get_next_link(batch_response.headers) - def send(self, request, **kwargs): - timeout = kwargs.get("timeout") - if timeout is None: - kwargs["timeout"] = self.timeout - return super().send(request, **kwargs) + +def combine_batches(all_results, batch_results, file_format): + if file_format == "json": + for key in ("results", "failedIds"): + if key in batch_results and batch_results[key]: + all_results[key] += batch_results[key] + elif file_format == "tsv": + return all_results + batch_results[1:] + else: + return all_results + batch_results + return all_results + + +def get_id_mapping_results_link(job_id): + url = f"{API_URL}/idmapping/details/{job_id}" + request = session.get(url) + check_response(request) + return request.json()["redirectURL"] + + +def decode_results(response, file_format, compressed): + if compressed: + decompressed = zlib.decompress(response.content, 16 + zlib.MAX_WBITS) + if file_format == "json": + j = json.loads(decompressed.decode("utf-8")) + return j + elif file_format == "tsv": + return [line for line in decompressed.decode("utf-8").split("\n") if line] + elif file_format == "xlsx": + return [decompressed] + elif file_format == "xml": + return [decompressed.decode("utf-8")] + else: + return decompressed.decode("utf-8") + elif file_format == "json": + return response.json() + elif file_format == "tsv": + return [line for line in response.text.split("\n") if line] + elif file_format == "xlsx": + return [response.content] + elif file_format == "xml": + return [response.text] + return response.text + + +def get_xml_namespace(element): + m = re.match(r"\{(.*)\}", element.tag) + return m.groups()[0] if m else "" + + +def merge_xml_results(xml_results): + merged_root = ElementTree.fromstring(xml_results[0]) + for result in xml_results[1:]: + root = ElementTree.fromstring(result) + for child in root.findall("{http://uniprot.org/uniprot}entry"): + merged_root.insert(-1, child) + ElementTree.register_namespace("", get_xml_namespace(merged_root[0])) + return ElementTree.tostring(merged_root, encoding="utf-8", xml_declaration=True) -def _map(query, f, t, format='tab', chunk_size=100): - """ _map is not meant for use with the python interface, use `map` instead - """ - tool = 'uploadlists/' - data = {'format': format, 'from': f, 'to': t} +def print_progress_batches(batch_index, size, total): + n_fetched = min((batch_index + 1) * size, total) + print(f"Fetched: {n_fetched} / {total}") + - req = [] - for i in range(0, len(query), chunk_size): - q = query[i:i + chunk_size] - req.append(dict([("url", URL + tool), - ('data', data), - ("files", {'file': ' '.join(q)})])) - return req - response = requests.post(URL + tool, data=data) - response.raise_for_status() - page = response.text - if "The service is temporarily unavailable" in page: - exit("The UNIPROT service is temporarily unavailable. Please try again later.") - return page +def get_id_mapping_results_search(url): + parsed = urlparse(url) + query = parse_qs(parsed.query) + file_format = query["format"][0] if "format" in query else "json" + if "size" in query: + size = int(query["size"][0]) + else: + size = 500 + query["size"] = size + compressed = ( + query["compressed"][0].lower() == "true" if "compressed" in query else False + ) + parsed = parsed._replace(query=urlencode(query, doseq=True)) + url = parsed.geturl() + request = session.get(url) + check_response(request) + results = decode_results(request, file_format, compressed) + total = int(request.headers["x-total-results"]) + print_progress_batches(0, size, total) + for i, batch in enumerate(get_batch(request, file_format, compressed), 1): + results = combine_batches(results, batch, file_format) + print_progress_batches(i, size, total) + if file_format == "xml": + return merge_xml_results(results) + return results -if __name__ == '__main__': - parser = argparse.ArgumentParser(description='retrieve uniprot mapping') - subparsers = parser.add_subparsers(dest='tool') +# print(results) +# {'results': [{'from': 'P05067', 'to': 'CHEMBL2487'}], 'failedIds': ['P12345']} + +if __name__ == "__main__": + parser = argparse.ArgumentParser(description="retrieve uniprot mapping") + subparsers = parser.add_subparsers(dest="tool") - mapping = subparsers.add_parser('map') - mapping.add_argument('f', help='from') - mapping.add_argument('t', help='to') - mapping.add_argument('inp', nargs='?', type=argparse.FileType('r'), - default=sys.stdin, help='input file (default: stdin)') - mapping.add_argument('out', nargs='?', type=argparse.FileType('w'), - default=sys.stdout, help='output file (default: stdout)') - mapping.add_argument('--format', default='tab', help='output format') + mapping = subparsers.add_parser("map") + mapping.add_argument("f", help="from") + mapping.add_argument("t", help="to") + mapping.add_argument( + "inp", + nargs="?", + type=argparse.FileType("r"), + default=sys.stdin, + help="input file (default: stdin)", + ) + mapping.add_argument( + "out", + nargs="?", + type=argparse.FileType("w"), + default=sys.stdout, + help="output file (default: stdout)", + ) + mapping.add_argument("--format", default="tab", help="output format") - retrieve = subparsers.add_parser('retrieve') - retrieve.add_argument('inp', metavar='in', nargs='?', type=argparse.FileType('r'), - default=sys.stdin, help='input file (default: stdin)') - retrieve.add_argument('out', nargs='?', type=argparse.FileType('w'), - default=sys.stdout, help='output file (default: stdout)') - retrieve.add_argument('-f', '--format', help='specify output format', default='txt') + retrieve = subparsers.add_parser("retrieve") + retrieve.add_argument( + "inp", + metavar="in", + nargs="?", + type=argparse.FileType("r"), + default=sys.stdin, + help="input file (default: stdin)", + ) + retrieve.add_argument( + "out", + nargs="?", + type=argparse.FileType("w"), + default=sys.stdout, + help="output file (default: stdout)", + ) + retrieve.add_argument("-f", "--format", help="specify output format", default="txt") + mapping = subparsers.add_parser("menu") args = parser.parse_args() + # code for auto generating the from - to conditional + if args.tool == "menu": + from lxml import etree + + request = session.get("https://rest.uniprot.org/configure/idmapping/fields") + check_response(request) + fields = request.json() + + tos = dict() + from_cond = etree.Element("conditional", name="from_cond") + from_select = etree.SubElement( + from_cond, "param", name="from", type="select", label="Source database:" + ) + + rules = dict() + for rule in fields["rules"]: + rules[rule["ruleId"]] = rule["tos"] + + for group in fields["groups"]: + group_name = group["groupName"] + group_name = group_name.replace("databases", "DBs") + for item in group["items"]: + if item["to"]: + tos[item["name"]] = f"{group_name} - {item['displayName']}" + + for group in fields["groups"]: + group_name = group["groupName"] + group_name = group_name.replace("databases", "DBs") + for item in group["items"]: + if not item["from"]: + continue + option = etree.SubElement(from_select, "option", value=item["name"]) + option.text = f"{group_name} - {item['displayName']}" + when = etree.SubElement(from_cond, "when", value=item["name"]) + + to_select = etree.SubElement( + when, "param", name="to", type="select", label="Target database:" + ) + ruleId = item["ruleId"] + for to in rules[ruleId]: + option = etree.SubElement(to_select, "option", value=to) + option.text = tos[to] + etree.indent(from_cond, space=" ") + print(etree.tostring(from_cond, pretty_print=True, encoding="unicode")) + sys.exit(0) + # get the IDs from the file as sorted list # (sorted is convenient for testing) query = set() @@ -94,15 +268,19 @@ query.add(line.strip()) query = sorted(query) - if args.tool == 'map': - pload = _map(query, args.f, args.t, chunk_size=100) - elif args.tool == 'retrieve': - pload = _map(query, 'ACC+ID', 'ACC', args.format, chunk_size=100) + if args.tool == "map": + job_id = submit_id_mapping(from_db=args.f, to_db=args.t, ids=query) + elif args.tool == "retrieve": + job_id = submit_id_mapping( + from_db="UniProtKB_AC-ID", to_db="UniProtKB", ids=query + ) - adapter = TimeoutHTTPAdapter(max_retries=retry_strategy) - http = requests.Session() - http.mount("https://", adapter) - for i, p in enumerate(pload): - response = http.post(**p) - args.out.write(response.text) - http.close() + if check_id_mapping_results_ready(job_id): + link = get_id_mapping_results_link(job_id) + link = f"{link}?format={args.format}" + print(link) + results = get_id_mapping_results_search(link) + + if not isinstance(results, str): + results = "\n".join(results) + args.out.write(f"{results}\n")
--- a/uniprot.xml Mon Nov 21 22:02:41 2022 +0000 +++ b/uniprot.xml Wed May 22 21:18:15 2024 +0000 @@ -1,197 +1,824 @@ -<tool id="uniprot" name="UniProt" version="0.4"> +<tool id="uniprot" name="UniProt" version="0.5" profile="23.1"> <description>ID mapping and retrieval</description> - <macros> - <import>macros.xml</import> - </macros> <requirements> <requirement type="package" version="2.25.1">requests</requirement> </requirements> <version_command>echo "UniProt ID mapping for Galaxy in version 0.1"</version_command> <command detect_errors="aggressive"><![CDATA[ - cut -f ${id_column} '$infile' > id_file.tabular && - '$__tool_directory__/uniprot.py' - + python '$__tool_directory__/uniprot.py' #if $tool.tool_choice == "retrieve": retrieve -f $tool.format id_file.tabular ./output #elif $tool.tool_choice == "map": map - - #if $tool.from.category_FROM == "uniprot" - '${tool.from.db_uniprot_FROM}' - #elif $tool.from.category_FROM == "oseqdb" - ${tool.from.db_oseqdb} - #elif $tool.from.category_FROM == "3Dstrdb" - ${tool.from.db_3Dstrdb} - #elif $tool.from.category_FROM == "ppidb" - ${tool.from.db_ppidb} - #elif $tool.from.category_FROM == "chemistry" - ${tool.from.db_chemistry} - #elif $tool.from.category_FROM == "protfgdb" - ${tool.from.db_protfgdb} - #elif $tool.from.category_FROM == "polymorphismANDmutation" - ${tool.from.db_polymorphismANDmutation} - #elif $tool.from.category_FROM == "2DgelDB" - ${tool.from.db_2DgelDB} - #elif $tool.from.category_FROM == "ProtocolsMaterialsDB" - ${tool.from.db_ProtocolsMaterialsDB} - #elif $tool.from.category_FROM == "GenomeAnnotationDB" - ${tool.from.db_GenomeAnnotationDB} - #elif $tool.from.category_FROM == "OrganismSpecificGeneDB" - ${tool.from.db_OrganismSpecificGeneDB} - #elif $tool.from.category_FROM == "phylogenomic" - ${tool.from.db_phylogenomic} - #elif $tool.from.category_FROM == "EnzymePathwayDB" - ${tool.from.db_EnzymePathwayDB} - #elif $tool.from.category_FROM == "GeneExpression" - ${tool.from.db_GeneExpression} - #elif $tool.from.category_FROM == "other" - ${tool.from.db_other} - #end if - - #if $tool.to.category_TO == "uniprot" - ${tool.to.db_uniprot_TO} - #elif $tool.to.category_TO == "oseqdb" - ${tool.to.db_oseqdb} - #elif $tool.to.category_TO == "3Dstrdb" - ${tool.to.db_3Dstrdb} - #elif $tool.to.category_TO == "ppidb" - ${tool.to.db_ppidb} - #elif $tool.to.category_TO == "chemistry" - ${tool.to.db_chemistry} - #elif $tool.to.category_TO == "protfgdb" - ${tool.to.db_protfgdb} - #elif $tool.to.category_TO == "polymorphismANDmutation" - ${tool.to.db_polymorphismANDmutation} - #elif $tool.to.category_TO == "2DgelDB" - ${tool.to.db_2DgelDB} - #elif $tool.to.category_TO == "ProtocolsMaterialsDB" - ${tool.to.db_ProtocolsMaterialsDB} - #elif $tool.to.category_TO == "GenomeAnnotationDB" - ${tool.to.db_GenomeAnnotationDB} - #elif $tool.to.category_TO == "OrganismSpecificGeneDB" - ${tool.to.db_OrganismSpecificGeneDB} - #elif $tool.to.category_TO == "phylogenomic" - ${tool.to.db_phylogenomic} - #elif $tool.to.category_TO == "EnzymePathwayDB" - ${tool.to.db_EnzymePathwayDB} - #elif $tool.to.category_TO == "GeneExpression" - ${tool.to.db_GeneExpression} - #elif $tool.to.category_TO == "other" - ${tool.to.db_other} - #end if - + --format tsv + "$from_cond.from" + "$from_cond.to" id_file.tabular ./output #end if - ]]></command> <inputs> <param name="infile" type="data" format="tabular" label="Input file with IDs" help="One ID in each line."/> <param name="id_column" label="ID column" type="data_column" data_ref="infile" help=""/> - <conditional name="tool"> <param name="tool_choice" type="select" label="Do you want to map IDs or retrieve data from UniProt" help=""> <option value="retrieve">Retrieve: request entries by uniprot accession using batch retrieval</option> <option value="map" selected="True">Map: map a list of ids from one format onto another using uniprots mapping API</option> </param> <when value="map"> - <conditional name="from"> - <expand macro="macro-category_FROM"/> - <when value="uniprot"> - <expand macro="macro-db_uniprot_FROM"/> - </when> - <when value="oseqdb"> - <expand macro="macro-db_oseqdb"/> - </when> - <when value="3Dstrdb"> - <expand macro="macro-db_3Dstrdb"/> - </when> - <when value="ppidb"> - <expand macro="macro-db_ppidb"/> - </when> - <when value="chemistry"> - <expand macro="macro-db_chemistry"/> - </when> - <when value="protfgdb"> - <expand macro="macro-db_protfgdb"/> - </when> - <when value="polymorphismANDmutation"> - <expand macro="macro-db_polymorphismANDmutation"/> + <!-- conditional auto generated with python tools/uniprot_rest_interface/uniprot.py menu --> + <conditional name="from_cond"> + <param name="from" type="select" label="Source database:"> + <option value="UniProtKB_AC-ID">UniProt - UniProtKB AC/ID</option> + <option value="UniParc">UniProt - UniParc</option> + <option value="UniRef50">UniProt - UniRef50</option> + <option value="UniRef90">UniProt - UniRef90</option> + <option value="UniRef100">UniProt - UniRef100</option> + <option value="Gene_Name">UniProt - Gene Name</option> + <option value="CRC64">UniProt - CRC64</option> + <option value="CCDS">Sequence DBs - CCDS</option> + <option value="EMBL-GenBank-DDBJ">Sequence DBs - EMBL/GenBank/DDBJ</option> + <option value="EMBL-GenBank-DDBJ_CDS">Sequence DBs - EMBL/GenBank/DDBJ CDS</option> + <option value="GI_number">Sequence DBs - GI number</option> + <option value="PIR">Sequence DBs - PIR</option> + <option value="RefSeq_Nucleotide">Sequence DBs - RefSeq Nucleotide</option> + <option value="RefSeq_Protein">Sequence DBs - RefSeq Protein</option> + <option value="PDB">3D structure DBs - PDB</option> + <option value="BioGRID">Protein-protein interaction DBs - BioGRID</option> + <option value="ComplexPortal">Protein-protein interaction DBs - ComplexPortal</option> + <option value="DIP">Protein-protein interaction DBs - DIP</option> + <option value="STRING">Protein-protein interaction DBs - STRING</option> + <option value="ChEMBL">Chemistry - ChEMBL</option> + <option value="DrugBank">Chemistry - DrugBank</option> + <option value="GuidetoPHARMACOLOGY">Chemistry - GuidetoPHARMACOLOGY</option> + <option value="SwissLipids">Chemistry - SwissLipids</option> + <option value="Allergome">Protein family/group DBs - Allergome</option> + <option value="CLAE">Protein family/group DBs - CLAE</option> + <option value="ESTHER">Protein family/group DBs - ESTHER</option> + <option value="MEROPS">Protein family/group DBs - MEROPS</option> + <option value="PeroxiBase">Protein family/group DBs - PeroxiBase</option> + <option value="REBASE">Protein family/group DBs - REBASE</option> + <option value="TCDB">Protein family/group DBs - TCDB</option> + <option value="GlyConnect">PTM DBs - GlyConnect</option> + <option value="BioMuta">Genetic variation DBs - BioMuta</option> + <option value="DMDM">Genetic variation DBs - DMDM</option> + <option value="World-2DPAGE">2D gel DBs - World-2DPAGE</option> + <option value="CPTAC">Proteomic DBs - CPTAC</option> + <option value="ProteomicsDB">Proteomic DBs - ProteomicsDB</option> + <option value="DNASU">Protocols and materials DBs - DNASU</option> + <option value="Ensembl">Genome annotation DBs - Ensembl</option> + <option value="Ensembl_Genomes">Genome annotation DBs - Ensembl Genomes</option> + <option value="Ensembl_Genomes_Protein">Genome annotation DBs - Ensembl Genomes Protein</option> + <option value="Ensembl_Genomes_Transcript">Genome annotation DBs - Ensembl Genomes Transcript</option> + <option value="Ensembl_Protein">Genome annotation DBs - Ensembl Protein</option> + <option value="Ensembl_Transcript">Genome annotation DBs - Ensembl Transcript</option> + <option value="GeneID">Genome annotation DBs - GeneID</option> + <option value="KEGG">Genome annotation DBs - KEGG</option> + <option value="PATRIC">Genome annotation DBs - PATRIC</option> + <option value="UCSC">Genome annotation DBs - UCSC</option> + <option value="WBParaSite">Genome annotation DBs - WBParaSite</option> + <option value="WBParaSite_Transcript-Protein">Genome annotation DBs - WBParaSite Transcript/Protein</option> + <option value="ArachnoServer">Organism-specific DBs - ArachnoServer</option> + <option value="Araport">Organism-specific DBs - Araport</option> + <option value="CGD">Organism-specific DBs - CGD</option> + <option value="ConoServer">Organism-specific DBs - ConoServer</option> + <option value="dictyBase">Organism-specific DBs - dictyBase</option> + <option value="EchoBASE">Organism-specific DBs - EchoBASE</option> + <option value="euHCVdb">Organism-specific DBs - euHCVdb</option> + <option value="FlyBase">Organism-specific DBs - FlyBase</option> + <option value="GeneCards">Organism-specific DBs - GeneCards</option> + <option value="GeneReviews">Organism-specific DBs - GeneReviews</option> + <option value="HGNC">Organism-specific DBs - HGNC</option> + <option value="LegioList">Organism-specific DBs - LegioList</option> + <option value="Leproma">Organism-specific DBs - Leproma</option> + <option value="MaizeGDB">Organism-specific DBs - MaizeGDB</option> + <option value="MGI">Organism-specific DBs - MGI</option> + <option value="MIM">Organism-specific DBs - MIM</option> + <option value="neXtProt">Organism-specific DBs - neXtProt</option> + <option value="OpenTargets">Organism-specific DBs - OpenTargets</option> + <option value="Orphanet">Organism-specific DBs - Orphanet</option> + <option value="PharmGKB">Organism-specific DBs - PharmGKB</option> + <option value="PomBase">Organism-specific DBs - PomBase</option> + <option value="PseudoCAP">Organism-specific DBs - PseudoCAP</option> + <option value="RGD">Organism-specific DBs - RGD</option> + <option value="SGD">Organism-specific DBs - SGD</option> + <option value="TubercuList">Organism-specific DBs - TubercuList</option> + <option value="VEuPathDB">Organism-specific DBs - VEuPathDB</option> + <option value="VGNC">Organism-specific DBs - VGNC</option> + <option value="WormBase">Organism-specific DBs - WormBase</option> + <option value="WormBase_Protein">Organism-specific DBs - WormBase Protein</option> + <option value="WormBase_Transcript">Organism-specific DBs - WormBase Transcript</option> + <option value="Xenbase">Organism-specific DBs - Xenbase</option> + <option value="ZFIN">Organism-specific DBs - ZFIN</option> + <option value="eggNOG">Phylogenomic DBs - eggNOG</option> + <option value="GeneTree">Phylogenomic DBs - GeneTree</option> + <option value="HOGENOM">Phylogenomic DBs - HOGENOM</option> + <option value="OMA">Phylogenomic DBs - OMA</option> + <option value="OrthoDB">Phylogenomic DBs - OrthoDB</option> + <option value="TreeFam">Phylogenomic DBs - TreeFam</option> + <option value="BioCyc">Enzyme and pathway DBs - BioCyc</option> + <option value="PlantReactome">Enzyme and pathway DBs - PlantReactome</option> + <option value="Reactome">Enzyme and pathway DBs - Reactome</option> + <option value="UniPathway">Enzyme and pathway DBs - UniPathway</option> + <option value="ChiTaRS">Miscellaneous - ChiTaRS</option> + <option value="GeneWiki">Miscellaneous - GeneWiki</option> + <option value="GenomeRNAi">Miscellaneous - GenomeRNAi</option> + <option value="PHI-base">Miscellaneous - PHI-base</option> + <option value="CollecTF">Gene expression DBs - CollecTF</option> + <option value="DisProt">Family and domain DBs - DisProt</option> + <option value="IDEAL">Family and domain DBs - IDEAL</option> + </param> + <when value="UniProtKB_AC-ID"> + <param name="to" type="select" label="Target database:"> + <option value="CCDS">Sequence DBs - CCDS</option> + <option value="PIR">Sequence DBs - PIR</option> + <option value="PDB">3D structure DBs - PDB</option> + <option value="BioGRID">Protein-protein interaction DBs - BioGRID</option> + <option value="ComplexPortal">Protein-protein interaction DBs - ComplexPortal</option> + <option value="DIP">Protein-protein interaction DBs - DIP</option> + <option value="STRING">Protein-protein interaction DBs - STRING</option> + <option value="ChEMBL">Chemistry - ChEMBL</option> + <option value="DrugBank">Chemistry - DrugBank</option> + <option value="GuidetoPHARMACOLOGY">Chemistry - GuidetoPHARMACOLOGY</option> + <option value="SwissLipids">Chemistry - SwissLipids</option> + <option value="Allergome">Protein family/group DBs - Allergome</option> + <option value="ESTHER">Protein family/group DBs - ESTHER</option> + <option value="MEROPS">Protein family/group DBs - MEROPS</option> + <option value="CLAE">Protein family/group DBs - CLAE</option> + <option value="PeroxiBase">Protein family/group DBs - PeroxiBase</option> + <option value="REBASE">Protein family/group DBs - REBASE</option> + <option value="TCDB">Protein family/group DBs - TCDB</option> + <option value="GlyConnect">PTM DBs - GlyConnect</option> + <option value="BioMuta">Genetic variation DBs - BioMuta</option> + <option value="DMDM">Genetic variation DBs - DMDM</option> + <option value="World-2DPAGE">2D gel DBs - World-2DPAGE</option> + <option value="CPTAC">Proteomic DBs - CPTAC</option> + <option value="ProteomicsDB">Proteomic DBs - ProteomicsDB</option> + <option value="DNASU">Protocols and materials DBs - DNASU</option> + <option value="Ensembl">Genome annotation DBs - Ensembl</option> + <option value="GeneID">Genome annotation DBs - GeneID</option> + <option value="KEGG">Genome annotation DBs - KEGG</option> + <option value="PATRIC">Genome annotation DBs - PATRIC</option> + <option value="UCSC">Genome annotation DBs - UCSC</option> + <option value="WBParaSite">Genome annotation DBs - WBParaSite</option> + <option value="ArachnoServer">Organism-specific DBs - ArachnoServer</option> + <option value="Araport">Organism-specific DBs - Araport</option> + <option value="CGD">Organism-specific DBs - CGD</option> + <option value="ConoServer">Organism-specific DBs - ConoServer</option> + <option value="dictyBase">Organism-specific DBs - dictyBase</option> + <option value="EchoBASE">Organism-specific DBs - EchoBASE</option> + <option value="euHCVdb">Organism-specific DBs - euHCVdb</option> + <option value="VEuPathDB">Organism-specific DBs - VEuPathDB</option> + <option value="FlyBase">Organism-specific DBs - FlyBase</option> + <option value="GeneCards">Organism-specific DBs - GeneCards</option> + <option value="GeneReviews">Organism-specific DBs - GeneReviews</option> + <option value="HGNC">Organism-specific DBs - HGNC</option> + <option value="LegioList">Organism-specific DBs - LegioList</option> + <option value="Leproma">Organism-specific DBs - Leproma</option> + <option value="MaizeGDB">Organism-specific DBs - MaizeGDB</option> + <option value="MGI">Organism-specific DBs - MGI</option> + <option value="MIM">Organism-specific DBs - MIM</option> + <option value="neXtProt">Organism-specific DBs - neXtProt</option> + <option value="OpenTargets">Organism-specific DBs - OpenTargets</option> + <option value="Orphanet">Organism-specific DBs - Orphanet</option> + <option value="PharmGKB">Organism-specific DBs - PharmGKB</option> + <option value="PomBase">Organism-specific DBs - PomBase</option> + <option value="PseudoCAP">Organism-specific DBs - PseudoCAP</option> + <option value="RGD">Organism-specific DBs - RGD</option> + <option value="SGD">Organism-specific DBs - SGD</option> + <option value="TubercuList">Organism-specific DBs - TubercuList</option> + <option value="VGNC">Organism-specific DBs - VGNC</option> + <option value="WormBase">Organism-specific DBs - WormBase</option> + <option value="Xenbase">Organism-specific DBs - Xenbase</option> + <option value="ZFIN">Organism-specific DBs - ZFIN</option> + <option value="eggNOG">Phylogenomic DBs - eggNOG</option> + <option value="GeneTree">Phylogenomic DBs - GeneTree</option> + <option value="HOGENOM">Phylogenomic DBs - HOGENOM</option> + <option value="OMA">Phylogenomic DBs - OMA</option> + <option value="OrthoDB">Phylogenomic DBs - OrthoDB</option> + <option value="TreeFam">Phylogenomic DBs - TreeFam</option> + <option value="BioCyc">Enzyme and pathway DBs - BioCyc</option> + <option value="Reactome">Enzyme and pathway DBs - Reactome</option> + <option value="UniPathway">Enzyme and pathway DBs - UniPathway</option> + <option value="PlantReactome">Enzyme and pathway DBs - PlantReactome</option> + <option value="ChiTaRS">Miscellaneous - ChiTaRS</option> + <option value="GeneWiki">Miscellaneous - GeneWiki</option> + <option value="GenomeRNAi">Miscellaneous - GenomeRNAi</option> + <option value="PHI-base">Miscellaneous - PHI-base</option> + <option value="CollecTF">Gene expression DBs - CollecTF</option> + <option value="IDEAL">Family and domain DBs - IDEAL</option> + <option value="DisProt">Family and domain DBs - DisProt</option> + <option value="UniProtKB">UniProt - UniProtKB</option> + <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> + <option value="UniParc">UniProt - UniParc</option> + <option value="UniRef50">UniProt - UniRef50</option> + <option value="UniRef90">UniProt - UniRef90</option> + <option value="UniRef100">UniProt - UniRef100</option> + <option value="Gene_Name">UniProt - Gene Name</option> + <option value="CRC64">UniProt - CRC64</option> + <option value="EMBL-GenBank-DDBJ">Sequence DBs - EMBL/GenBank/DDBJ</option> + <option value="EMBL-GenBank-DDBJ_CDS">Sequence DBs - EMBL/GenBank/DDBJ CDS</option> + <option value="GI_number">Sequence DBs - GI number</option> + <option value="RefSeq_Nucleotide">Sequence DBs - RefSeq Nucleotide</option> + <option value="RefSeq_Protein">Sequence DBs - RefSeq Protein</option> + <option value="Ensembl_Protein">Genome annotation DBs - Ensembl Protein</option> + <option value="Ensembl_Transcript">Genome annotation DBs - Ensembl Transcript</option> + <option value="Ensembl_Genomes">Genome annotation DBs - Ensembl Genomes</option> + <option value="Ensembl_Genomes_Protein">Genome annotation DBs - Ensembl Genomes Protein</option> + <option value="Ensembl_Genomes_Transcript">Genome annotation DBs - Ensembl Genomes Transcript</option> + <option value="WBParaSite_Transcript-Protein">Genome annotation DBs - WBParaSite Transcript/Protein</option> + <option value="WormBase_Protein">Organism-specific DBs - WormBase Protein</option> + <option value="WormBase_Transcript">Organism-specific DBs - WormBase Transcript</option> + </param> </when> - <when value="2DgelDB"> - <expand macro="macro-db_2DgelDB"/> + <when value="UniParc"> + <param name="to" type="select" label="Target database:"> + <option value="UniProtKB">UniProt - UniProtKB</option> + <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> + <option value="UniParc">UniProt - UniParc</option> + </param> + </when> + <when value="UniRef50"> + <param name="to" type="select" label="Target database:"> + <option value="UniProtKB">UniProt - UniProtKB</option> + <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> + <option value="UniRef50">UniProt - UniRef50</option> + </param> + </when> + <when value="UniRef90"> + <param name="to" type="select" label="Target database:"> + <option value="UniProtKB">UniProt - UniProtKB</option> + <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> + <option value="UniRef90">UniProt - UniRef90</option> + </param> </when> - <when value="ProtocolsMaterialsDB"> - <expand macro="macro-db_ProtocolsMaterialsDB"/> + <when value="UniRef100"> + <param name="to" type="select" label="Target database:"> + <option value="UniProtKB">UniProt - UniProtKB</option> + <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> + <option value="UniRef100">UniProt - UniRef100</option> + </param> + </when> + <when value="Gene_Name"> + <param name="to" type="select" label="Target database:"> + <option value="UniProtKB">UniProt - UniProtKB</option> + <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> + </param> + </when> + <when value="CRC64"> + <param name="to" type="select" label="Target database:"> + <option value="UniProtKB">UniProt - UniProtKB</option> + <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> + </param> + </when> + <when value="CCDS"> + <param name="to" type="select" label="Target database:"> + <option value="UniProtKB">UniProt - UniProtKB</option> + <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> + </param> </when> - <when value="GenomeAnnotationDB"> - <expand macro="macro-db_GenomeAnnotationDB"/> + <when value="EMBL-GenBank-DDBJ"> + <param name="to" type="select" label="Target database:"> + <option value="UniProtKB">UniProt - UniProtKB</option> + <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> + </param> + </when> + <when value="EMBL-GenBank-DDBJ_CDS"> + <param name="to" type="select" label="Target database:"> + <option value="UniProtKB">UniProt - UniProtKB</option> + <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> + </param> + </when> + <when value="GI_number"> + <param name="to" type="select" label="Target database:"> + <option value="UniProtKB">UniProt - UniProtKB</option> + <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> + </param> + </when> + <when value="PIR"> + <param name="to" type="select" label="Target database:"> + <option value="UniProtKB">UniProt - UniProtKB</option> + <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> + </param> </when> - <when value="OrganismSpecificGeneDB"> - <expand macro="macro-db_OrganismSpecificGeneDB"/> + <when value="RefSeq_Nucleotide"> + <param name="to" type="select" label="Target database:"> + <option value="UniProtKB">UniProt - UniProtKB</option> + <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> + </param> + </when> + <when value="RefSeq_Protein"> + <param name="to" type="select" label="Target database:"> + <option value="UniProtKB">UniProt - UniProtKB</option> + <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> + </param> + </when> + <when value="PDB"> + <param name="to" type="select" label="Target database:"> + <option value="UniProtKB">UniProt - UniProtKB</option> + <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> + </param> + </when> + <when value="BioGRID"> + <param name="to" type="select" label="Target database:"> + <option value="UniProtKB">UniProt - UniProtKB</option> + <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> + </param> </when> - <when value="phylogenomic"> - <expand macro="macro-db_phylogenomic"/> + <when value="ComplexPortal"> + <param name="to" type="select" label="Target database:"> + <option value="UniProtKB">UniProt - UniProtKB</option> + <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> + </param> + </when> + <when value="DIP"> + <param name="to" type="select" label="Target database:"> + <option value="UniProtKB">UniProt - UniProtKB</option> + <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> + </param> + </when> + <when value="STRING"> + <param name="to" type="select" label="Target database:"> + <option value="UniProtKB">UniProt - UniProtKB</option> + <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> + </param> + </when> + <when value="ChEMBL"> + <param name="to" type="select" label="Target database:"> + <option value="UniProtKB">UniProt - UniProtKB</option> + <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> + </param> </when> - <when value="EnzymePathwayDB"> - <expand macro="macro-db_EnzymePathwayDB"/> + <when value="DrugBank"> + <param name="to" type="select" label="Target database:"> + <option value="UniProtKB">UniProt - UniProtKB</option> + <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> + </param> + </when> + <when value="GuidetoPHARMACOLOGY"> + <param name="to" type="select" label="Target database:"> + <option value="UniProtKB">UniProt - UniProtKB</option> + <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> + </param> + </when> + <when value="SwissLipids"> + <param name="to" type="select" label="Target database:"> + <option value="UniProtKB">UniProt - UniProtKB</option> + <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> + </param> + </when> + <when value="Allergome"> + <param name="to" type="select" label="Target database:"> + <option value="UniProtKB">UniProt - UniProtKB</option> + <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> + </param> </when> - <when value="GeneExpression"> - <expand macro="macro-db_GeneExpression"/> + <when value="CLAE"> + <param name="to" type="select" label="Target database:"> + <option value="UniProtKB">UniProt - UniProtKB</option> + <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> + </param> + </when> + <when value="ESTHER"> + <param name="to" type="select" label="Target database:"> + <option value="UniProtKB">UniProt - UniProtKB</option> + <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> + </param> + </when> + <when value="MEROPS"> + <param name="to" type="select" label="Target database:"> + <option value="UniProtKB">UniProt - UniProtKB</option> + <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> + </param> + </when> + <when value="PeroxiBase"> + <param name="to" type="select" label="Target database:"> + <option value="UniProtKB">UniProt - UniProtKB</option> + <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> + </param> </when> - <when value="other"> - <expand macro="macro-db_other"/> + <when value="REBASE"> + <param name="to" type="select" label="Target database:"> + <option value="UniProtKB">UniProt - UniProtKB</option> + <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> + </param> + </when> + <when value="TCDB"> + <param name="to" type="select" label="Target database:"> + <option value="UniProtKB">UniProt - UniProtKB</option> + <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> + </param> + </when> + <when value="GlyConnect"> + <param name="to" type="select" label="Target database:"> + <option value="UniProtKB">UniProt - UniProtKB</option> + <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> + </param> + </when> + <when value="BioMuta"> + <param name="to" type="select" label="Target database:"> + <option value="UniProtKB">UniProt - UniProtKB</option> + <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> + </param> </when> - </conditional> - <conditional name="to"> - <expand macro="macro-category_TO"/> - <when value="uniprot"> - <expand macro="macro-db_uniprot_TO"/> + <when value="DMDM"> + <param name="to" type="select" label="Target database:"> + <option value="UniProtKB">UniProt - UniProtKB</option> + <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> + </param> + </when> + <when value="World-2DPAGE"> + <param name="to" type="select" label="Target database:"> + <option value="UniProtKB">UniProt - UniProtKB</option> + <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> + </param> + </when> + <when value="CPTAC"> + <param name="to" type="select" label="Target database:"> + <option value="UniProtKB">UniProt - UniProtKB</option> + <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> + </param> + </when> + <when value="ProteomicsDB"> + <param name="to" type="select" label="Target database:"> + <option value="UniProtKB">UniProt - UniProtKB</option> + <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> + </param> + </when> + <when value="DNASU"> + <param name="to" type="select" label="Target database:"> + <option value="UniProtKB">UniProt - UniProtKB</option> + <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> + </param> + </when> + <when value="Ensembl"> + <param name="to" type="select" label="Target database:"> + <option value="UniProtKB">UniProt - UniProtKB</option> + <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> + </param> + </when> + <when value="Ensembl_Genomes"> + <param name="to" type="select" label="Target database:"> + <option value="UniProtKB">UniProt - UniProtKB</option> + <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> + </param> + </when> + <when value="Ensembl_Genomes_Protein"> + <param name="to" type="select" label="Target database:"> + <option value="UniProtKB">UniProt - UniProtKB</option> + <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> + </param> </when> - <when value="oseqdb"> - <expand macro="macro-db_oseqdb"/> + <when value="Ensembl_Genomes_Transcript"> + <param name="to" type="select" label="Target database:"> + <option value="UniProtKB">UniProt - UniProtKB</option> + <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> + </param> + </when> + <when value="Ensembl_Protein"> + <param name="to" type="select" label="Target database:"> + <option value="UniProtKB">UniProt - UniProtKB</option> + <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> + </param> + </when> + <when value="Ensembl_Transcript"> + <param name="to" type="select" label="Target database:"> + <option value="UniProtKB">UniProt - UniProtKB</option> + <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> + </param> + </when> + <when value="GeneID"> + <param name="to" type="select" label="Target database:"> + <option value="UniProtKB">UniProt - UniProtKB</option> + <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> + </param> </when> - <when value="3Dstrdb"> - <expand macro="macro-db_3Dstrdb"/> + <when value="KEGG"> + <param name="to" type="select" label="Target database:"> + <option value="UniProtKB">UniProt - UniProtKB</option> + <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> + </param> + </when> + <when value="PATRIC"> + <param name="to" type="select" label="Target database:"> + <option value="UniProtKB">UniProt - UniProtKB</option> + <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> + </param> + </when> + <when value="UCSC"> + <param name="to" type="select" label="Target database:"> + <option value="UniProtKB">UniProt - UniProtKB</option> + <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> + </param> + </when> + <when value="WBParaSite"> + <param name="to" type="select" label="Target database:"> + <option value="UniProtKB">UniProt - UniProtKB</option> + <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> + </param> </when> - <when value="ppidb"> - <expand macro="macro-db_ppidb"/> + <when value="WBParaSite_Transcript-Protein"> + <param name="to" type="select" label="Target database:"> + <option value="UniProtKB">UniProt - UniProtKB</option> + <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> + </param> + </when> + <when value="ArachnoServer"> + <param name="to" type="select" label="Target database:"> + <option value="UniProtKB">UniProt - UniProtKB</option> + <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> + </param> + </when> + <when value="Araport"> + <param name="to" type="select" label="Target database:"> + <option value="UniProtKB">UniProt - UniProtKB</option> + <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> + </param> + </when> + <when value="CGD"> + <param name="to" type="select" label="Target database:"> + <option value="UniProtKB">UniProt - UniProtKB</option> + <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> + </param> </when> - <when value="chemistry"> - <expand macro="macro-db_chemistry"/> + <when value="ConoServer"> + <param name="to" type="select" label="Target database:"> + <option value="UniProtKB">UniProt - UniProtKB</option> + <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> + </param> + </when> + <when value="dictyBase"> + <param name="to" type="select" label="Target database:"> + <option value="UniProtKB">UniProt - UniProtKB</option> + <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> + </param> + </when> + <when value="EchoBASE"> + <param name="to" type="select" label="Target database:"> + <option value="UniProtKB">UniProt - UniProtKB</option> + <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> + </param> + </when> + <when value="euHCVdb"> + <param name="to" type="select" label="Target database:"> + <option value="UniProtKB">UniProt - UniProtKB</option> + <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> + </param> </when> - <when value="protfgdb"> - <expand macro="macro-db_protfgdb"/> + <when value="FlyBase"> + <param name="to" type="select" label="Target database:"> + <option value="UniProtKB">UniProt - UniProtKB</option> + <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> + </param> + </when> + <when value="GeneCards"> + <param name="to" type="select" label="Target database:"> + <option value="UniProtKB">UniProt - UniProtKB</option> + <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> + </param> + </when> + <when value="GeneReviews"> + <param name="to" type="select" label="Target database:"> + <option value="UniProtKB">UniProt - UniProtKB</option> + <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> + </param> + </when> + <when value="HGNC"> + <param name="to" type="select" label="Target database:"> + <option value="UniProtKB">UniProt - UniProtKB</option> + <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> + </param> </when> - <when value="polymorphismANDmutation"> - <expand macro="macro-db_polymorphismANDmutation"/> + <when value="LegioList"> + <param name="to" type="select" label="Target database:"> + <option value="UniProtKB">UniProt - UniProtKB</option> + <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> + </param> + </when> + <when value="Leproma"> + <param name="to" type="select" label="Target database:"> + <option value="UniProtKB">UniProt - UniProtKB</option> + <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> + </param> + </when> + <when value="MaizeGDB"> + <param name="to" type="select" label="Target database:"> + <option value="UniProtKB">UniProt - UniProtKB</option> + <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> + </param> + </when> + <when value="MGI"> + <param name="to" type="select" label="Target database:"> + <option value="UniProtKB">UniProt - UniProtKB</option> + <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> + </param> + </when> + <when value="MIM"> + <param name="to" type="select" label="Target database:"> + <option value="UniProtKB">UniProt - UniProtKB</option> + <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> + </param> </when> - <when value="2DgelDB"> - <expand macro="macro-db_2DgelDB"/> + <when value="neXtProt"> + <param name="to" type="select" label="Target database:"> + <option value="UniProtKB">UniProt - UniProtKB</option> + <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> + </param> + </when> + <when value="OpenTargets"> + <param name="to" type="select" label="Target database:"> + <option value="UniProtKB">UniProt - UniProtKB</option> + <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> + </param> + </when> + <when value="Orphanet"> + <param name="to" type="select" label="Target database:"> + <option value="UniProtKB">UniProt - UniProtKB</option> + <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> + </param> + </when> + <when value="PharmGKB"> + <param name="to" type="select" label="Target database:"> + <option value="UniProtKB">UniProt - UniProtKB</option> + <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> + </param> </when> - <when value="ProtocolsMaterialsDB"> - <expand macro="macro-db_ProtocolsMaterialsDB"/> + <when value="PomBase"> + <param name="to" type="select" label="Target database:"> + <option value="UniProtKB">UniProt - UniProtKB</option> + <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> + </param> + </when> + <when value="PseudoCAP"> + <param name="to" type="select" label="Target database:"> + <option value="UniProtKB">UniProt - UniProtKB</option> + <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> + </param> + </when> + <when value="RGD"> + <param name="to" type="select" label="Target database:"> + <option value="UniProtKB">UniProt - UniProtKB</option> + <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> + </param> + </when> + <when value="SGD"> + <param name="to" type="select" label="Target database:"> + <option value="UniProtKB">UniProt - UniProtKB</option> + <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> + </param> </when> - <when value="GenomeAnnotationDB"> - <expand macro="macro-db_GenomeAnnotationDB"/> + <when value="TubercuList"> + <param name="to" type="select" label="Target database:"> + <option value="UniProtKB">UniProt - UniProtKB</option> + <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> + </param> + </when> + <when value="VEuPathDB"> + <param name="to" type="select" label="Target database:"> + <option value="UniProtKB">UniProt - UniProtKB</option> + <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> + </param> + </when> + <when value="VGNC"> + <param name="to" type="select" label="Target database:"> + <option value="UniProtKB">UniProt - UniProtKB</option> + <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> + </param> + </when> + <when value="WormBase"> + <param name="to" type="select" label="Target database:"> + <option value="UniProtKB">UniProt - UniProtKB</option> + <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> + </param> </when> - <when value="OrganismSpecificGeneDB"> - <expand macro="macro-db_OrganismSpecificGeneDB"/> + <when value="WormBase_Protein"> + <param name="to" type="select" label="Target database:"> + <option value="UniProtKB">UniProt - UniProtKB</option> + <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> + </param> + </when> + <when value="WormBase_Transcript"> + <param name="to" type="select" label="Target database:"> + <option value="UniProtKB">UniProt - UniProtKB</option> + <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> + </param> + </when> + <when value="Xenbase"> + <param name="to" type="select" label="Target database:"> + <option value="UniProtKB">UniProt - UniProtKB</option> + <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> + </param> + </when> + <when value="ZFIN"> + <param name="to" type="select" label="Target database:"> + <option value="UniProtKB">UniProt - UniProtKB</option> + <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> + </param> </when> - <when value="phylogenomic"> - <expand macro="macro-db_phylogenomic"/> + <when value="eggNOG"> + <param name="to" type="select" label="Target database:"> + <option value="UniProtKB">UniProt - UniProtKB</option> + <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> + </param> + </when> + <when value="GeneTree"> + <param name="to" type="select" label="Target database:"> + <option value="UniProtKB">UniProt - UniProtKB</option> + <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> + </param> + </when> + <when value="HOGENOM"> + <param name="to" type="select" label="Target database:"> + <option value="UniProtKB">UniProt - UniProtKB</option> + <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> + </param> + </when> + <when value="OMA"> + <param name="to" type="select" label="Target database:"> + <option value="UniProtKB">UniProt - UniProtKB</option> + <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> + </param> </when> - <when value="EnzymePathwayDB"> - <expand macro="macro-db_EnzymePathwayDB"/> + <when value="OrthoDB"> + <param name="to" type="select" label="Target database:"> + <option value="UniProtKB">UniProt - UniProtKB</option> + <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> + </param> + </when> + <when value="TreeFam"> + <param name="to" type="select" label="Target database:"> + <option value="UniProtKB">UniProt - UniProtKB</option> + <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> + </param> + </when> + <when value="BioCyc"> + <param name="to" type="select" label="Target database:"> + <option value="UniProtKB">UniProt - UniProtKB</option> + <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> + </param> + </when> + <when value="PlantReactome"> + <param name="to" type="select" label="Target database:"> + <option value="UniProtKB">UniProt - UniProtKB</option> + <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> + </param> </when> - <when value="GeneExpression"> - <expand macro="macro-db_GeneExpression"/> + <when value="Reactome"> + <param name="to" type="select" label="Target database:"> + <option value="UniProtKB">UniProt - UniProtKB</option> + <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> + </param> + </when> + <when value="UniPathway"> + <param name="to" type="select" label="Target database:"> + <option value="UniProtKB">UniProt - UniProtKB</option> + <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> + </param> + </when> + <when value="ChiTaRS"> + <param name="to" type="select" label="Target database:"> + <option value="UniProtKB">UniProt - UniProtKB</option> + <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> + </param> + </when> + <when value="GeneWiki"> + <param name="to" type="select" label="Target database:"> + <option value="UniProtKB">UniProt - UniProtKB</option> + <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> + </param> </when> - <when value="other"> - <expand macro="macro-db_other"/> + <when value="GenomeRNAi"> + <param name="to" type="select" label="Target database:"> + <option value="UniProtKB">UniProt - UniProtKB</option> + <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> + </param> + </when> + <when value="PHI-base"> + <param name="to" type="select" label="Target database:"> + <option value="UniProtKB">UniProt - UniProtKB</option> + <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> + </param> + </when> + <when value="CollecTF"> + <param name="to" type="select" label="Target database:"> + <option value="UniProtKB">UniProt - UniProtKB</option> + <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> + </param> + </when> + <when value="DisProt"> + <param name="to" type="select" label="Target database:"> + <option value="UniProtKB">UniProt - UniProtKB</option> + <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> + </param> + </when> + <when value="IDEAL"> + <param name="to" type="select" label="Target database:"> + <option value="UniProtKB">UniProt - UniProtKB</option> + <option value="UniProtKB-Swiss-Prot">UniProt - UniProtKB/Swiss-Prot</option> + </param> </when> </conditional> </when> @@ -206,58 +833,54 @@ </inputs> <outputs> <data name="outfile_retrieve_fasta" format="fasta" from_work_dir="./output" - label="${tool.name} on ${on_string} (retrieve output)"> + label="${tool.name} on ${on_string}: fasta"> <filter>tool['tool_choice'] == 'retrieve'</filter> <filter>tool['format'] == 'fasta'</filter> </data> <data name="outfile_retrieve_gff" format="gff" from_work_dir="./output" - label="${tool.name} on ${on_string} (retrieve output)"> + label="${tool.name} on ${on_string}: gff"> <filter>tool['tool_choice'] == 'retrieve'</filter> <filter>tool['format'] == 'gff'</filter> </data> <data name="outfile_retrieve_txt" format="txt" from_work_dir="./output" - label="${tool.name} on ${on_string} (retrieve output)"> + label="${tool.name} on ${on_string}: txt"> <filter>tool['tool_choice'] == 'retrieve'</filter> <filter>tool['format'] == 'txt'</filter> </data> <data name="outfile_map" format="tabular" from_work_dir="./output" - label="${tool.name} on ${on_string} (map output)"> + label="${tool.name} on ${on_string}: mapping"> <filter>tool['tool_choice'] == 'map'</filter> </data> </outputs> <tests> - <test> + <test expect_num_outputs="1"> <param name="infile" value="id_uniprot.tab" ftype="tabular"/> <param name="id_column" value="c1"/> <param name="format" value="fasta"/> <param name="tool_choice" value="retrieve"/> <output name="outfile_retrieve_fasta" file="test1_retrieve.fasta" ftype="fasta" compare="sim_size" /> </test> - <test> + <test expect_num_outputs="1"> <param name="infile" value="id_uniprot.tab" ftype="tabular"/> <param name="id_column" value="c1"/> <param name="format" value="gff"/> <param name="tool_choice" value="retrieve"/> <output name="outfile_retrieve_gff" file="test2_retrieve.gff" ftype="gff" compare="sim_size" /> </test> - <test> + <test expect_num_outputs="1"> <param name="infile" value="id_uniprot.tab" ftype="tabular"/> <param name="id_column" value="c1"/> <param name="tool_choice" value="map"/> - <param name="category_FROM" value="uniprot"/> - <param name="db_uniprot_FROM" value="ID"/> - <param name="category_TO" value="uniprot"/> - <param name="db_uniprot_TO" value="GENENAME"/> + <param name="from" value="UniProtKB_AC-ID"/> + <param name="to" value="Gene_Name"/> <output name="outfile_map" file="test1_map.tab" ftype="tabular"/> </test> - <test> + <test expect_num_outputs="1"> <param name="infile" value="id_map_refseq.txt" ftype="tabular"/> <param name="id_column" value="c1"/> <param name="tool_choice" value="map"/> - <param name="category_FROM" value="oseqdb"/> - <param name="db_oseqdb" value="REFSEQ_NT_ID"/> - <param name="category_TO" value="uniprot"/> - <param name="db_uniprot_TO" value="ID"/> + <param name="from" value="RefSeq_Nucleotide"/> + <param name="to" value="UniProtKB"/> <output name="outfile_map" file="test2_map.tab" ftype="tabular"/> </test> </tests>