Mercurial > repos > iuc > ncbi_eutils_esearch
changeset 3:49b8084df3ce draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 041f11d6eb83568deda382857b121274dffe9825
| author | iuc |
|---|---|
| date | Fri, 10 Jun 2016 14:49:25 -0400 |
| parents | 0ea34f262410 |
| children | 258f8ed9a08b |
| files | __efetch_build_options.py elink.py esearch.xml eutils.py eutils.pyc macros.xml |
| diffstat | 6 files changed, 772 insertions(+), 239 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/__efetch_build_options.py Fri Jun 10 14:49:25 2016 -0400 @@ -0,0 +1,267 @@ +#!/usr/bin/env python +# Daniel Blankenberg +# Creates the options for tool interface +import re + +# http://eutils.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi +db_list = ''' +<DbName>annotinfo</DbName> +<DbName>assembly</DbName> +<DbName>bioproject</DbName> +<DbName>biosample</DbName> +<DbName>biosystems</DbName> +<DbName>blastdbinfo</DbName> +<DbName>books</DbName> +<DbName>cdd</DbName> +<DbName>clinvar</DbName> +<DbName>clone</DbName> +<DbName>dbvar</DbName> +<DbName>gap</DbName> +<DbName>gapplus</DbName> +<DbName>gds</DbName> +<DbName>gencoll</DbName> +<DbName>gene</DbName> +<DbName>genome</DbName> +<DbName>geoprofiles</DbName> +<DbName>grasp</DbName> +<DbName>gtr</DbName> +<DbName>homologene</DbName> +<DbName>medgen</DbName> +<DbName>mesh</DbName> +<DbName>ncbisearch</DbName> +<DbName>nlmcatalog</DbName> +<DbName>nuccore</DbName> +<DbName>nucest</DbName> +<DbName>nucgss</DbName> +<DbName>nucleotide</DbName> +<DbName>omim</DbName> +<DbName>orgtrack</DbName> +<DbName>pcassay</DbName> +<DbName>pccompound</DbName> +<DbName>pcsubstance</DbName> +<DbName>pmc</DbName> +<DbName>popset</DbName> +<DbName>probe</DbName> +<DbName>protein</DbName> +<DbName>proteinclusters</DbName> +<DbName>pubmed</DbName> +<DbName>pubmedhealth</DbName> +<DbName>seqannot</DbName> +<DbName>snp</DbName> +<DbName>sra</DbName> +<DbName>structure</DbName> +<DbName>taxonomy</DbName> +<DbName>unigene</DbName>'''.replace( "<DbName>", "").replace( "</DbName>", "").split("\n") + + +help = ''' (all) + docsum xml Document Summary + docsum json Document Summary + full text Full Document + uilist xml Unique Identifier List + uilist text Unique Identifier List + full xml Full Document + + bioproject + native BioProject Report + native xml RecordSet + + biosample + native BioSample Report + native xml BioSampleSet + + biosystems + native xml Sys-set + + gds + native xml RecordSet + summary text Summary + + gene + gene_table xml Gene Table + native text Gene Report + native asn.1 Entrezgene + native xml Entrezgene-Set + tabular tabular Tabular Report + + homologene + alignmentscores text Alignment Scores + fasta fasta FASTA + homologene text Homologene Report + native text Homologene List + native asn.1 HG-Entry + native xml Entrez-Homologene-Set + + mesh + full text Full Record + native text MeSH Report + native xml RecordSet + + nlmcatalog + native text Full Record + native xml NLMCatalogRecordSet + + pmc + medline text MEDLINE + native xml pmc-articleset + + pubmed + abstract xml Abstract + medline text MEDLINE + native asn.1 Pubmed-entry + native xml PubmedArticleSet + + (sequences) + acc text Accession Number + est xml EST Report + fasta fasta FASTA + fasta xml TinySeq + fasta_cds_aa fasta CDS Products + fasta_cds_na fasta Coding Regions + ft text Feature Table + gb text GenBank Flatfile + gb xml GBSet + gbc xml INSDSet + gbwithparts text GenBank with Contig Sequences + gene_fasta fasta FASTA of Gene + gp text GenPept Flatfile + gp xml GBSet + gpc xml INSDSet + gss text GSS Report + ipg text Identical Protein Report + ipg xml IPGReportSet + native text Seq-entry + native xml Bioseq-set + seqid asn.1 Seq-id + + snp + chr text Chromosome Report + docset text Summary + fasta fasta FASTA + flt text Flat File + native asn.1 Rs + native xml ExchangeSet + rsr tabular RS Cluster Report + ssexemplar text SS Exemplar List + + sra + native xml EXPERIMENT_PACKAGE_SET + runinfo xml SraRunInfo + + structure + mmdb asn.1 Ncbi-mime-asn1 strucseq + native text MMDB Report + native xml RecordSet + + taxonomy + native text Taxonomy List + native xml TaxaSet'''.split("\n") + + +db = {} +for db_name in db_list: + db[db_name] = [] + +section = None +for line in help: + line = re.split('\s{2,}', line.strip()) + # Ignore empties + if len(line) == 0: + continue + # Section headers have one item + elif len(line) == 1: + section = line[0] + db[section] = [] + # Format lines have 2+ + elif len(line) == 2: + parent_format = line[0] + description = line[1] + + if parent_format not in db[section]: + db[section].append((parent_format, None, description)) + elif len(line) == 3: + parent_format = line[0] + format_modifier = line[1] + description = line[2] + + if parent_format not in db[section]: + db[section].append((parent_format, format_modifier, description)) + + +all_formats = db['(all)'] +del db['(all)'] +sequences_formats = db['(sequences)'] +del db['(sequences)'] +del db[''] + +for key in db: + db[key] += all_formats + +for key in ('nuccore', 'nucest', 'nucgss', 'nucleotide'): + db[key] += sequences_formats + +MACRO_TPL = ''' + +''' + +WHEN_TPL = ''' <when value="{format}"> + <param name="output_format" type="select" label="Output Format"> + {format_options} + </param> + </when>''' + +FORMAT_OPTION_TPL = '''<option value="{name_type}">{name_type_human}</option>''' + +format_names = {} + +print ''' <xml name="db"> + <conditional name="db"> + <expand macro="dbselect" />''' +for key in sorted(db): + format_options = [] + + for (parent_format, format_modifier, description) in sorted(db[key]): + name_human = description + if format_modifier: + name_human += ' (%s)' % format_modifier + format_string = '%s-%s' % (parent_format, format_modifier) + + format_options.append(FORMAT_OPTION_TPL.format( + name_type=format_string, + name_type_human=name_human, + )) + + format_names[format_string] = format_modifier + + print WHEN_TPL.format( + format=key, + format_options='\n '.join(format_options) + ) + +print ''' </conditional> + </xml>''' + +CHANGE_FORMAT_TPL = ''' + <xml name="efetch_formats"> + <change_format> + {formats} + </change_format> + </xml> +''' + +CHANGE_FORMAT_WHEN_TPL = '''<when input="output_format" value="{key}" format="{value}"/>''' +# Format options + + +whens = [] +for (k, v) in format_names.items(): + if v is None: + v = 'text' + elif v == 'asn.1': + v = 'asn1' + + whens.append(CHANGE_FORMAT_WHEN_TPL.format( + key=k, value=v + )) + +print CHANGE_FORMAT_TPL.format(formats='\n '.join(whens))
--- a/elink.py Thu Apr 07 17:38:52 2016 -0400 +++ b/elink.py Fri Jun 10 14:49:25 2016 -0400 @@ -1,7 +1,8 @@ #!/usr/bin/env python import argparse +import json + import eutils -import json if __name__ == '__main__': @@ -9,8 +10,8 @@ parser.add_argument('db', help='Database to use, sometimes "none" (e.g. *check)') parser.add_argument('dbfrom', help='Database containing input UIDs') parser.add_argument('cmd', choices=['neighbor', 'neighbor_score', - 'neighbor_history', 'acheck', 'ncheck', 'lcheck', - 'llinks', 'llinkslib', 'prlinks'], + 'neighbor_history', 'acheck', 'ncheck', 'lcheck', + 'llinks', 'llinkslib', 'prlinks'], help='ELink command mode') # Only used in case of neighbor_history parser.add_argument('--history_out', type=argparse.FileType('w'),
--- a/esearch.xml Thu Apr 07 17:38:52 2016 -0400 +++ b/esearch.xml Fri Jun 10 14:49:25 2016 -0400 @@ -14,8 +14,6 @@ --history_file $history_file #end if -$use_history - #if $date.enabled: --datetype $date.datetype
--- a/eutils.py Thu Apr 07 17:38:52 2016 -0400 +++ b/eutils.py Fri Jun 10 14:49:25 2016 -0400 @@ -27,6 +27,7 @@ if history_file is not None: with open(history_file, 'r') as handle: data = json.loads(handle.read()) + print data self.query_key = data['QueryKey'] self.webenv = data['WebEnv'] self.using_history = True
--- a/macros.xml Thu Apr 07 17:38:52 2016 -0400 +++ b/macros.xml Fri Jun 10 14:49:25 2016 -0400 @@ -1,6 +1,6 @@ <?xml version="1.0"?> <macros> - <token name="@WRAPPER_VERSION@">1.0</token> + <token name="@WRAPPER_VERSION@">1.1</token> <token name="@EMAIL_ARGUMENTS@"> --user_email "$__user_email__" #set admin_emails = ';'.join(str($__admin_users__).split(',')) @@ -90,6 +90,7 @@ token_label="NCBI Database to Use" > <param name="@NAME@" type="select" label="@LABEL@"> + <option value="annotinfo">Annotation Information</option> <option value="assembly">Assembly</option> <option value="bioproject">BioProject</option> <option value="biosample">BioSample</option> @@ -100,23 +101,26 @@ <option value="clinvar">Clinical Variants</option> <option value="clone">CLone</option> <option value="dbvar">dbVar</option> - <option value="epigenomics">Epigenomics</option> <option value="gap">dbGaP</option> + <option value="gapplus">gapplus</option> <option value="gds">GEO Datasets</option> + <option value="gencoll">Gencoll</option> <option value="gene">Gene</option> <option value="genome">Genome</option> <option value="geoprofiles">GEO Profiles</option> + <option value="grasp">grasp</option> <option value="gtr">Genetic Testing Registry</option> <option value="homologene">HomoloGene</option> - <option value="journals">Journals</option> <option value="medgen">MedGen</option> <option value="mesh">MeSH</option> <option value="ncbisearch">NCBI Web Site</option> <option value="nlmcatalog">NLM Catalog</option> - <option value="nuccore">Nucleotide</option> + <option value="nuccore">Nuccore</option> <option value="nucest">EST</option> <option value="nucgss">GSS</option> + <option value="nucleotide">Nucleotide</option> <option value="omim">OMIM</option> + <option value="orgtrack">Orgtrack</option> <option value="pcassay">PubChem BioAssay</option> <option value="pccompound">PubChem Compound</option> <option value="pcsubstance">PubChem Substance</option> @@ -127,403 +131,665 @@ <option value="proteinclusters">Protein Clusters</option> <option value="pubmed">PubMed</option> <option value="pubmedhealth">PubMed Health</option> + <option value="seqannot">seqannot</option> <option value="snp">SNP</option> <option value="sra">SRA</option> <option value="structure">Structure</option> <option value="taxonomy">Taxonomy</option> - <option value="toolkit">NCBI C++ Toolkit</option> - <option value="toolkitall">NCBI C++ Toolkit All</option> - <option value="toolkitbook">NCBI C++ Toolkit Book</option> <option value="unigene">UniGene</option> </param> </xml> <xml name="db"> <conditional name="db"> <expand macro="dbselect" /> + <when value="annotinfo"> + <param name="output_format" type="select" label="Output Format"> + <option value="docsum-json">Document Summary (json)</option> + <option value="docsum-xml">Document Summary (xml)</option> + <option value="full-text">Full Document (text)</option> + <option value="full-xml">Full Document (xml)</option> + <option value="uilist-text">Unique Identifier List (text)</option> + <option value="uilist-xml">Unique Identifier List (xml)</option> + </param> + </when> <when value="assembly"> <param name="output_format" type="select" label="Output Format"> - <option value="docsum-xml">Document summary</option> - <option value="uilist-xml">List of UIDs (XML)</option> - <option value="uilist-text">List of UIDs (plain text)</option> + <option value="docsum-json">Document Summary (json)</option> + <option value="docsum-xml">Document Summary (xml)</option> + <option value="full-text">Full Document (text)</option> + <option value="full-xml">Full Document (xml)</option> + <option value="uilist-text">Unique Identifier List (text)</option> + <option value="uilist-xml">Unique Identifier List (xml)</option> </param> </when> <when value="bioproject"> <param name="output_format" type="select" label="Output Format"> - <option value="docsum-xml">Document summary</option> - <option value="uilist-xml">List of UIDs (XML)</option> - <option value="uilist-text">List of UIDs (plain text)</option> - <option value="xml-xml">Full record</option> + <option value="docsum-json">Document Summary (json)</option> + <option value="docsum-xml">Document Summary (xml)</option> + <option value="full-text">Full Document (text)</option> + <option value="full-xml">Full Document (xml)</option> + <option value="native-None">BioProject Report</option> + <option value="native-xml">RecordSet (xml)</option> + <option value="uilist-text">Unique Identifier List (text)</option> + <option value="uilist-xml">Unique Identifier List (xml)</option> </param> </when> <when value="biosample"> <param name="output_format" type="select" label="Output Format"> - <option value="docsum-xml">Document summary</option> - <option value="uilist-xml">List of UIDs (XML)</option> - <option value="uilist-text">List of UIDs (plain text)</option> - <option value="full-xml">Full record (XML)</option> - <option value="full-text">Full record (plain text)</option> + <option value="docsum-json">Document Summary (json)</option> + <option value="docsum-xml">Document Summary (xml)</option> + <option value="full-text">Full Document (text)</option> + <option value="full-xml">Full Document (xml)</option> + <option value="native-None">BioSample Report</option> + <option value="native-xml">BioSampleSet (xml)</option> + <option value="uilist-text">Unique Identifier List (text)</option> + <option value="uilist-xml">Unique Identifier List (xml)</option> </param> </when> <when value="biosystems"> <param name="output_format" type="select" label="Output Format"> - <option value="docsum-xml">Document summary</option> - <option value="uilist-xml">List of UIDs (XML)</option> - <option value="uilist-text">List of UIDs (plain text)</option> - <option value="xml-xml">Full record</option> + <option value="docsum-json">Document Summary (json)</option> + <option value="docsum-xml">Document Summary (xml)</option> + <option value="full-text">Full Document (text)</option> + <option value="full-xml">Full Document (xml)</option> + <option value="native-xml">Sys-set (xml)</option> + <option value="uilist-text">Unique Identifier List (text)</option> + <option value="uilist-xml">Unique Identifier List (xml)</option> </param> </when> <when value="blastdbinfo"> <param name="output_format" type="select" label="Output Format"> - <option value="docsum-xml">Document summary</option> - <option value="uilist-xml">List of UIDs (XML)</option> - <option value="uilist-text">List of UIDs (plain text)</option> + <option value="docsum-json">Document Summary (json)</option> + <option value="docsum-xml">Document Summary (xml)</option> + <option value="full-text">Full Document (text)</option> + <option value="full-xml">Full Document (xml)</option> + <option value="uilist-text">Unique Identifier List (text)</option> + <option value="uilist-xml">Unique Identifier List (xml)</option> </param> </when> <when value="books"> <param name="output_format" type="select" label="Output Format"> - <option value="docsum-xml">Document summary</option> - <option value="uilist-xml">List of UIDs (XML)</option> - <option value="uilist-text">List of UIDs (plain text)</option> + <option value="docsum-json">Document Summary (json)</option> + <option value="docsum-xml">Document Summary (xml)</option> + <option value="full-text">Full Document (text)</option> + <option value="full-xml">Full Document (xml)</option> + <option value="uilist-text">Unique Identifier List (text)</option> + <option value="uilist-xml">Unique Identifier List (xml)</option> </param> </when> <when value="cdd"> <param name="output_format" type="select" label="Output Format"> - <option value="docsum-xml">Document summary</option> - <option value="uilist-xml">List of UIDs (XML)</option> - <option value="uilist-text">List of UIDs (plain text)</option> + <option value="docsum-json">Document Summary (json)</option> + <option value="docsum-xml">Document Summary (xml)</option> + <option value="full-text">Full Document (text)</option> + <option value="full-xml">Full Document (xml)</option> + <option value="uilist-text">Unique Identifier List (text)</option> + <option value="uilist-xml">Unique Identifier List (xml)</option> </param> </when> <when value="clinvar"> <param name="output_format" type="select" label="Output Format"> - <option value="docsum-xml">Document summary</option> - <option value="uilist-xml">List of UIDs (XML)</option> - <option value="uilist-text">List of UIDs (plain text)</option> + <option value="docsum-json">Document Summary (json)</option> + <option value="docsum-xml">Document Summary (xml)</option> + <option value="full-text">Full Document (text)</option> + <option value="full-xml">Full Document (xml)</option> + <option value="uilist-text">Unique Identifier List (text)</option> + <option value="uilist-xml">Unique Identifier List (xml)</option> </param> </when> <when value="clone"> <param name="output_format" type="select" label="Output Format"> - <option value="docsum-xml">Document summary</option> - <option value="uilist-xml">List of UIDs (XML)</option> - <option value="uilist-text">List of UIDs (plain text)</option> + <option value="docsum-json">Document Summary (json)</option> + <option value="docsum-xml">Document Summary (xml)</option> + <option value="full-text">Full Document (text)</option> + <option value="full-xml">Full Document (xml)</option> + <option value="uilist-text">Unique Identifier List (text)</option> + <option value="uilist-xml">Unique Identifier List (xml)</option> </param> </when> <when value="dbvar"> <param name="output_format" type="select" label="Output Format"> - <option value="docsum-xml">Document summary</option> - <option value="uilist-xml">List of UIDs (XML)</option> - <option value="uilist-text">List of UIDs (plain text)</option> - </param> - </when> - <when value="epigenomics"> - <param name="output_format" type="select" label="Output Format"> - <option value="docsum-xml">Document summary</option> - <option value="uilist-xml">List of UIDs (XML)</option> - <option value="uilist-text">List of UIDs (plain text)</option> + <option value="docsum-json">Document Summary (json)</option> + <option value="docsum-xml">Document Summary (xml)</option> + <option value="full-text">Full Document (text)</option> + <option value="full-xml">Full Document (xml)</option> + <option value="uilist-text">Unique Identifier List (text)</option> + <option value="uilist-xml">Unique Identifier List (xml)</option> </param> </when> <when value="gap"> <param name="output_format" type="select" label="Output Format"> - <option value="docsum-xml">Document summary</option> - <option value="uilist-xml">List of UIDs (XML)</option> - <option value="uilist-text">List of UIDs (plain text)</option> + <option value="docsum-json">Document Summary (json)</option> + <option value="docsum-xml">Document Summary (xml)</option> + <option value="full-text">Full Document (text)</option> + <option value="full-xml">Full Document (xml)</option> + <option value="uilist-text">Unique Identifier List (text)</option> + <option value="uilist-xml">Unique Identifier List (xml)</option> + </param> + </when> + <when value="gapplus"> + <param name="output_format" type="select" label="Output Format"> + <option value="docsum-json">Document Summary (json)</option> + <option value="docsum-xml">Document Summary (xml)</option> + <option value="full-text">Full Document (text)</option> + <option value="full-xml">Full Document (xml)</option> + <option value="uilist-text">Unique Identifier List (text)</option> + <option value="uilist-xml">Unique Identifier List (xml)</option> </param> </when> <when value="gds"> <param name="output_format" type="select" label="Output Format"> - <option value="docsum-xml">Document summary</option> - <option value="uilist-xml">List of UIDs (XML)</option> - <option value="uilist-text">List of UIDs (plain text)</option> - <option value="summary-text">Summary</option> + <option value="docsum-json">Document Summary (json)</option> + <option value="docsum-xml">Document Summary (xml)</option> + <option value="full-text">Full Document (text)</option> + <option value="full-xml">Full Document (xml)</option> + <option value="native-xml">RecordSet (xml)</option> + <option value="summary-text">Summary (text)</option> + <option value="uilist-text">Unique Identifier List (text)</option> + <option value="uilist-xml">Unique Identifier List (xml)</option> + </param> + </when> + <when value="gencoll"> + <param name="output_format" type="select" label="Output Format"> + <option value="docsum-json">Document Summary (json)</option> + <option value="docsum-xml">Document Summary (xml)</option> + <option value="full-text">Full Document (text)</option> + <option value="full-xml">Full Document (xml)</option> + <option value="uilist-text">Unique Identifier List (text)</option> + <option value="uilist-xml">Unique Identifier List (xml)</option> </param> </when> <when value="gene"> <param name="output_format" type="select" label="Output Format"> - <option value="docsum-xml">Document summary</option> - <option value="uilist-xml">List of UIDs (XML)</option> - <option value="uilist-text">List of UIDs (plain text)</option> - <option value="null-asn.1">text (ASN.1)</option> - <option value="null-xml">XML</option> - <option value="gene_table-text">Gene table</option> + <option value="docsum-json">Document Summary (json)</option> + <option value="docsum-xml">Document Summary (xml)</option> + <option value="full-text">Full Document (text)</option> + <option value="full-xml">Full Document (xml)</option> + <option value="gene_table-xml">Gene Table (xml)</option> + <option value="native-asn.1">Entrezgene (asn.1)</option> + <option value="native-text">Gene Report (text)</option> + <option value="native-xml">Entrezgene-Set (xml)</option> + <option value="tabular-tabular">Tabular Report (tabular)</option> + <option value="uilist-text">Unique Identifier List (text)</option> + <option value="uilist-xml">Unique Identifier List (xml)</option> </param> </when> <when value="genome"> <param name="output_format" type="select" label="Output Format"> - <option value="docsum-xml">Document summary</option> - <option value="uilist-xml">List of UIDs (XML)</option> - <option value="uilist-text">List of UIDs (plain text)</option> + <option value="docsum-json">Document Summary (json)</option> + <option value="docsum-xml">Document Summary (xml)</option> + <option value="full-text">Full Document (text)</option> + <option value="full-xml">Full Document (xml)</option> + <option value="uilist-text">Unique Identifier List (text)</option> + <option value="uilist-xml">Unique Identifier List (xml)</option> </param> </when> <when value="geoprofiles"> <param name="output_format" type="select" label="Output Format"> - <option value="docsum-xml">Document summary</option> - <option value="uilist-xml">List of UIDs (XML)</option> - <option value="uilist-text">List of UIDs (plain text)</option> + <option value="docsum-json">Document Summary (json)</option> + <option value="docsum-xml">Document Summary (xml)</option> + <option value="full-text">Full Document (text)</option> + <option value="full-xml">Full Document (xml)</option> + <option value="uilist-text">Unique Identifier List (text)</option> + <option value="uilist-xml">Unique Identifier List (xml)</option> + </param> + </when> + <when value="grasp"> + <param name="output_format" type="select" label="Output Format"> + <option value="docsum-json">Document Summary (json)</option> + <option value="docsum-xml">Document Summary (xml)</option> + <option value="full-text">Full Document (text)</option> + <option value="full-xml">Full Document (xml)</option> + <option value="uilist-text">Unique Identifier List (text)</option> + <option value="uilist-xml">Unique Identifier List (xml)</option> </param> </when> <when value="gtr"> <param name="output_format" type="select" label="Output Format"> - <option value="docsum-xml">Document summary</option> - <option value="uilist-xml">List of UIDs (XML)</option> - <option value="uilist-text">List of UIDs (plain text)</option> + <option value="docsum-json">Document Summary (json)</option> + <option value="docsum-xml">Document Summary (xml)</option> + <option value="full-text">Full Document (text)</option> + <option value="full-xml">Full Document (xml)</option> + <option value="uilist-text">Unique Identifier List (text)</option> + <option value="uilist-xml">Unique Identifier List (xml)</option> </param> </when> <when value="homologene"> <param name="output_format" type="select" label="Output Format"> - <option value="docsum-xml">Document summary</option> - <option value="uilist-xml">List of UIDs (XML)</option> - <option value="uilist-text">List of UIDs (plain text)</option> - <option value="null-asn.1">text ASN.1</option> - <option value="null-xml">XML</option> - <option value="alignmentscores-text">Alignment scores</option> - <option value="fasta-text">FASTA</option> - <option value="homologene-text">HomoloGene</option> - </param> - </when> - <when value="journals"> - <param name="output_format" type="select" label="Output Format"> - <option value="docsum-xml">Document summary</option> - <option value="uilist-xml">List of UIDs (XML)</option> - <option value="uilist-text">List of UIDs (plain text)</option> + <option value="alignmentscores-text">Alignment Scores (text)</option> + <option value="docsum-json">Document Summary (json)</option> + <option value="docsum-xml">Document Summary (xml)</option> + <option value="fasta-fasta">FASTA (fasta)</option> + <option value="full-text">Full Document (text)</option> + <option value="full-xml">Full Document (xml)</option> + <option value="homologene-text">Homologene Report (text)</option> + <option value="native-asn.1">HG-Entry (asn.1)</option> + <option value="native-text">Homologene List (text)</option> + <option value="native-xml">Entrez-Homologene-Set (xml)</option> + <option value="uilist-text">Unique Identifier List (text)</option> + <option value="uilist-xml">Unique Identifier List (xml)</option> </param> </when> <when value="medgen"> <param name="output_format" type="select" label="Output Format"> - <option value="docsum-xml">Document summary</option> - <option value="uilist-xml">List of UIDs (XML)</option> - <option value="uilist-text">List of UIDs (plain text)</option> + <option value="docsum-json">Document Summary (json)</option> + <option value="docsum-xml">Document Summary (xml)</option> + <option value="full-text">Full Document (text)</option> + <option value="full-xml">Full Document (xml)</option> + <option value="uilist-text">Unique Identifier List (text)</option> + <option value="uilist-xml">Unique Identifier List (xml)</option> </param> </when> <when value="mesh"> <param name="output_format" type="select" label="Output Format"> - <option value="docsum-xml">Document summary</option> - <option value="uilist-xml">List of UIDs (XML)</option> - <option value="uilist-text">List of UIDs (plain text)</option> - <option value="full-text">Full record</option> + <option value="docsum-json">Document Summary (json)</option> + <option value="docsum-xml">Document Summary (xml)</option> + <option value="full-text">Full Document (text)</option> + <option value="full-text">Full Record (text)</option> + <option value="full-xml">Full Document (xml)</option> + <option value="native-text">MeSH Report (text)</option> + <option value="native-xml">RecordSet (xml)</option> + <option value="uilist-text">Unique Identifier List (text)</option> + <option value="uilist-xml">Unique Identifier List (xml)</option> </param> </when> <when value="ncbisearch"> <param name="output_format" type="select" label="Output Format"> - <option value="docsum-xml">Document summary</option> - <option value="uilist-xml">List of UIDs (XML)</option> - <option value="uilist-text">List of UIDs (plain text)</option> + <option value="docsum-json">Document Summary (json)</option> + <option value="docsum-xml">Document Summary (xml)</option> + <option value="full-text">Full Document (text)</option> + <option value="full-xml">Full Document (xml)</option> + <option value="uilist-text">Unique Identifier List (text)</option> + <option value="uilist-xml">Unique Identifier List (xml)</option> </param> </when> <when value="nlmcatalog"> <param name="output_format" type="select" label="Output Format"> - <option value="docsum-xml">Document summary</option> - <option value="uilist-xml">List of UIDs (XML)</option> - <option value="uilist-text">List of UIDs (plain text)</option> - <option value="null-text">Full record</option> - <option value="null-xml">XML</option> + <option value="docsum-json">Document Summary (json)</option> + <option value="docsum-xml">Document Summary (xml)</option> + <option value="full-text">Full Document (text)</option> + <option value="full-xml">Full Document (xml)</option> + <option value="native-text">Full Record (text)</option> + <option value="native-xml">NLMCatalogRecordSet (xml)</option> + <option value="uilist-text">Unique Identifier List (text)</option> + <option value="uilist-xml">Unique Identifier List (xml)</option> </param> </when> <when value="nuccore"> <param name="output_format" type="select" label="Output Format"> - <option value="docsum-xml">Document summary</option> - <option value="uilist-xml">List of UIDs (XML)</option> - <option value="uilist-text">List of UIDs (plain text)</option> - <option value="null-text">text ASN.1</option> - <option value="null-asn.1">binary ASN.1</option> - <option value="native-xml">Full record in XML</option> - <option value="acc-text">Accession number(s)</option> - <option value="fasta-text">FASTA</option> - <option value="fasta-xml">TinySeq XML</option> - <option value="seqid-text">SeqID string</option> - <option value="gb-text">GenBank flat file</option> - <option value="gb-xml">GBSeq XML</option> - <option value="gbc-xml">INSDSeq XML</option> - <option value="ft-text">Feature table</option> - <option value="gbwithparts-text">GenBank flat file with full sequence (contigs)</option> - <option value="fasta_cds_na-text">CDS nucleotide FASTA</option> - <option value="fasta_cds_aa-text">CDS protein FASTA</option> + <option value="acc-text">Accession Number (text)</option> + <option value="docsum-json">Document Summary (json)</option> + <option value="docsum-xml">Document Summary (xml)</option> + <option value="est-xml">EST Report (xml)</option> + <option value="fasta-fasta">FASTA (fasta)</option> + <option value="fasta-xml">TinySeq (xml)</option> + <option value="fasta_cds_aa-fasta">CDS Products (fasta)</option> + <option value="fasta_cds_na-fasta">Coding Regions (fasta)</option> + <option value="ft-text">Feature Table (text)</option> + <option value="full-text">Full Document (text)</option> + <option value="full-xml">Full Document (xml)</option> + <option value="gb-text">GenBank Flatfile (text)</option> + <option value="gb-xml">GBSet (xml)</option> + <option value="gbc-xml">INSDSet (xml)</option> + <option value="gbwithparts-text">GenBank with Contig Sequences (text)</option> + <option value="gene_fasta-fasta">FASTA of Gene (fasta)</option> + <option value="gp-text">GenPept Flatfile (text)</option> + <option value="gp-xml">GBSet (xml)</option> + <option value="gpc-xml">INSDSet (xml)</option> + <option value="gss-text">GSS Report (text)</option> + <option value="ipg-text">Identical Protein Report (text)</option> + <option value="ipg-xml">IPGReportSet (xml)</option> + <option value="native-text">Seq-entry (text)</option> + <option value="native-xml">Bioseq-set (xml)</option> + <option value="seqid-asn.1">Seq-id (asn.1)</option> + <option value="uilist-text">Unique Identifier List (text)</option> + <option value="uilist-xml">Unique Identifier List (xml)</option> </param> </when> <when value="nucest"> <param name="output_format" type="select" label="Output Format"> - <option value="docsum-xml">Document summary</option> - <option value="uilist-xml">List of UIDs (XML)</option> - <option value="uilist-text">List of UIDs (plain text)</option> - <option value="null-text">text ASN.1</option> - <option value="null-asn.1">binary ASN.1</option> - <option value="native-xml">Full record in XML</option> - <option value="acc-text">Accession number(s)</option> - <option value="fasta-text">FASTA</option> - <option value="fasta-xml">TinySeq XML</option> - <option value="seqid-text">SeqID string</option> - <option value="gb-text">GenBank flat file</option> - <option value="gb-xml">GBSeq XML</option> - <option value="gbc-xml">INSDSeq XML</option> - <option value="est-text">EST report</option> + <option value="acc-text">Accession Number (text)</option> + <option value="docsum-json">Document Summary (json)</option> + <option value="docsum-xml">Document Summary (xml)</option> + <option value="est-xml">EST Report (xml)</option> + <option value="fasta-fasta">FASTA (fasta)</option> + <option value="fasta-xml">TinySeq (xml)</option> + <option value="fasta_cds_aa-fasta">CDS Products (fasta)</option> + <option value="fasta_cds_na-fasta">Coding Regions (fasta)</option> + <option value="ft-text">Feature Table (text)</option> + <option value="full-text">Full Document (text)</option> + <option value="full-xml">Full Document (xml)</option> + <option value="gb-text">GenBank Flatfile (text)</option> + <option value="gb-xml">GBSet (xml)</option> + <option value="gbc-xml">INSDSet (xml)</option> + <option value="gbwithparts-text">GenBank with Contig Sequences (text)</option> + <option value="gene_fasta-fasta">FASTA of Gene (fasta)</option> + <option value="gp-text">GenPept Flatfile (text)</option> + <option value="gp-xml">GBSet (xml)</option> + <option value="gpc-xml">INSDSet (xml)</option> + <option value="gss-text">GSS Report (text)</option> + <option value="ipg-text">Identical Protein Report (text)</option> + <option value="ipg-xml">IPGReportSet (xml)</option> + <option value="native-text">Seq-entry (text)</option> + <option value="native-xml">Bioseq-set (xml)</option> + <option value="seqid-asn.1">Seq-id (asn.1)</option> + <option value="uilist-text">Unique Identifier List (text)</option> + <option value="uilist-xml">Unique Identifier List (xml)</option> </param> </when> <when value="nucgss"> <param name="output_format" type="select" label="Output Format"> - <option value="docsum-xml">Document summary</option> - <option value="uilist-xml">List of UIDs (XML)</option> - <option value="uilist-text">List of UIDs (plain text)</option> - <option value="null-text">text ASN.1</option> - <option value="null-asn.1">binary ASN.1</option> - <option value="native-xml">Full record in XML</option> - <option value="acc-text">Accession number(s)</option> - <option value="fasta-text">FASTA</option> - <option value="fasta-xml">TinySeq XML</option> - <option value="seqid-text">SeqID string</option> - <option value="gb-text">GenBank flat file</option> - <option value="gb-xml">GBSeq XML</option> - <option value="gbc-xml">INSDSeq XML</option> - <option value="gss-text">GSS report</option> + <option value="acc-text">Accession Number (text)</option> + <option value="docsum-json">Document Summary (json)</option> + <option value="docsum-xml">Document Summary (xml)</option> + <option value="est-xml">EST Report (xml)</option> + <option value="fasta-fasta">FASTA (fasta)</option> + <option value="fasta-xml">TinySeq (xml)</option> + <option value="fasta_cds_aa-fasta">CDS Products (fasta)</option> + <option value="fasta_cds_na-fasta">Coding Regions (fasta)</option> + <option value="ft-text">Feature Table (text)</option> + <option value="full-text">Full Document (text)</option> + <option value="full-xml">Full Document (xml)</option> + <option value="gb-text">GenBank Flatfile (text)</option> + <option value="gb-xml">GBSet (xml)</option> + <option value="gbc-xml">INSDSet (xml)</option> + <option value="gbwithparts-text">GenBank with Contig Sequences (text)</option> + <option value="gene_fasta-fasta">FASTA of Gene (fasta)</option> + <option value="gp-text">GenPept Flatfile (text)</option> + <option value="gp-xml">GBSet (xml)</option> + <option value="gpc-xml">INSDSet (xml)</option> + <option value="gss-text">GSS Report (text)</option> + <option value="ipg-text">Identical Protein Report (text)</option> + <option value="ipg-xml">IPGReportSet (xml)</option> + <option value="native-text">Seq-entry (text)</option> + <option value="native-xml">Bioseq-set (xml)</option> + <option value="seqid-asn.1">Seq-id (asn.1)</option> + <option value="uilist-text">Unique Identifier List (text)</option> + <option value="uilist-xml">Unique Identifier List (xml)</option> + </param> + </when> + <when value="nucleotide"> + <param name="output_format" type="select" label="Output Format"> + <option value="acc-text">Accession Number (text)</option> + <option value="docsum-json">Document Summary (json)</option> + <option value="docsum-xml">Document Summary (xml)</option> + <option value="est-xml">EST Report (xml)</option> + <option value="fasta-fasta">FASTA (fasta)</option> + <option value="fasta-xml">TinySeq (xml)</option> + <option value="fasta_cds_aa-fasta">CDS Products (fasta)</option> + <option value="fasta_cds_na-fasta">Coding Regions (fasta)</option> + <option value="ft-text">Feature Table (text)</option> + <option value="full-text">Full Document (text)</option> + <option value="full-xml">Full Document (xml)</option> + <option value="gb-text">GenBank Flatfile (text)</option> + <option value="gb-xml">GBSet (xml)</option> + <option value="gbc-xml">INSDSet (xml)</option> + <option value="gbwithparts-text">GenBank with Contig Sequences (text)</option> + <option value="gene_fasta-fasta">FASTA of Gene (fasta)</option> + <option value="gp-text">GenPept Flatfile (text)</option> + <option value="gp-xml">GBSet (xml)</option> + <option value="gpc-xml">INSDSet (xml)</option> + <option value="gss-text">GSS Report (text)</option> + <option value="ipg-text">Identical Protein Report (text)</option> + <option value="ipg-xml">IPGReportSet (xml)</option> + <option value="native-text">Seq-entry (text)</option> + <option value="native-xml">Bioseq-set (xml)</option> + <option value="seqid-asn.1">Seq-id (asn.1)</option> + <option value="uilist-text">Unique Identifier List (text)</option> + <option value="uilist-xml">Unique Identifier List (xml)</option> </param> </when> <when value="omim"> <param name="output_format" type="select" label="Output Format"> - <option value="docsum-xml">Document summary</option> - <option value="uilist-xml">List of UIDs (XML)</option> - <option value="uilist-text">List of UIDs (plain text)</option> + <option value="docsum-json">Document Summary (json)</option> + <option value="docsum-xml">Document Summary (xml)</option> + <option value="full-text">Full Document (text)</option> + <option value="full-xml">Full Document (xml)</option> + <option value="uilist-text">Unique Identifier List (text)</option> + <option value="uilist-xml">Unique Identifier List (xml)</option> + </param> + </when> + <when value="orgtrack"> + <param name="output_format" type="select" label="Output Format"> + <option value="docsum-json">Document Summary (json)</option> + <option value="docsum-xml">Document Summary (xml)</option> + <option value="full-text">Full Document (text)</option> + <option value="full-xml">Full Document (xml)</option> + <option value="uilist-text">Unique Identifier List (text)</option> + <option value="uilist-xml">Unique Identifier List (xml)</option> </param> </when> <when value="pcassay"> <param name="output_format" type="select" label="Output Format"> - <option value="docsum-xml">Document summary</option> - <option value="uilist-xml">List of UIDs (XML)</option> - <option value="uilist-text">List of UIDs (plain text)</option> + <option value="docsum-json">Document Summary (json)</option> + <option value="docsum-xml">Document Summary (xml)</option> + <option value="full-text">Full Document (text)</option> + <option value="full-xml">Full Document (xml)</option> + <option value="uilist-text">Unique Identifier List (text)</option> + <option value="uilist-xml">Unique Identifier List (xml)</option> </param> </when> <when value="pccompound"> <param name="output_format" type="select" label="Output Format"> - <option value="docsum-xml">Document summary</option> - <option value="uilist-xml">List of UIDs (XML)</option> - <option value="uilist-text">List of UIDs (plain text)</option> + <option value="docsum-json">Document Summary (json)</option> + <option value="docsum-xml">Document Summary (xml)</option> + <option value="full-text">Full Document (text)</option> + <option value="full-xml">Full Document (xml)</option> + <option value="uilist-text">Unique Identifier List (text)</option> + <option value="uilist-xml">Unique Identifier List (xml)</option> </param> </when> <when value="pcsubstance"> <param name="output_format" type="select" label="Output Format"> - <option value="docsum-xml">Document summary</option> - <option value="uilist-xml">List of UIDs (XML)</option> - <option value="uilist-text">List of UIDs (plain text)</option> + <option value="docsum-json">Document Summary (json)</option> + <option value="docsum-xml">Document Summary (xml)</option> + <option value="full-text">Full Document (text)</option> + <option value="full-xml">Full Document (xml)</option> + <option value="uilist-text">Unique Identifier List (text)</option> + <option value="uilist-xml">Unique Identifier List (xml)</option> </param> </when> <when value="pmc"> <param name="output_format" type="select" label="Output Format"> - <option value="docsum-xml">Document summary</option> - <option value="uilist-xml">List of UIDs (XML)</option> - <option value="uilist-text">List of UIDs (plain text)</option> - <option value="null-xml">XML</option> - <option value="medline-text">MEDLINE</option> + <option value="docsum-json">Document Summary (json)</option> + <option value="docsum-xml">Document Summary (xml)</option> + <option value="full-text">Full Document (text)</option> + <option value="full-xml">Full Document (xml)</option> + <option value="medline-text">MEDLINE (text)</option> + <option value="native-xml">pmc-articleset (xml)</option> + <option value="uilist-text">Unique Identifier List (text)</option> + <option value="uilist-xml">Unique Identifier List (xml)</option> </param> </when> <when value="popset"> <param name="output_format" type="select" label="Output Format"> - <option value="docsum-xml">Document summary</option> - <option value="uilist-xml">List of UIDs (XML)</option> - <option value="uilist-text">List of UIDs (plain text)</option> - <option value="null-text">text ASN.1</option> - <option value="null-asn.1">binary ASN.1</option> - <option value="native-xml">Full record in XML</option> - <option value="acc-text">Accession number(s)</option> - <option value="fasta-text">FASTA</option> - <option value="fasta-xml">TinySeq XML</option> - <option value="seqid-text">SeqID string</option> - <option value="gb-text">GenBank flat file</option> - <option value="gb-xml">GBSeq XML</option> - <option value="gbc-xml">INSDSeq XML</option> + <option value="docsum-json">Document Summary (json)</option> + <option value="docsum-xml">Document Summary (xml)</option> + <option value="full-text">Full Document (text)</option> + <option value="full-xml">Full Document (xml)</option> + <option value="uilist-text">Unique Identifier List (text)</option> + <option value="uilist-xml">Unique Identifier List (xml)</option> </param> </when> <when value="probe"> <param name="output_format" type="select" label="Output Format"> - <option value="docsum-xml">Document summary</option> - <option value="uilist-xml">List of UIDs (XML)</option> - <option value="uilist-text">List of UIDs (plain text)</option> + <option value="docsum-json">Document Summary (json)</option> + <option value="docsum-xml">Document Summary (xml)</option> + <option value="full-text">Full Document (text)</option> + <option value="full-xml">Full Document (xml)</option> + <option value="uilist-text">Unique Identifier List (text)</option> + <option value="uilist-xml">Unique Identifier List (xml)</option> </param> </when> <when value="protein"> <param name="output_format" type="select" label="Output Format"> - <option value="docsum-xml">Document summary</option> - <option value="uilist-xml">List of UIDs (XML)</option> - <option value="uilist-text">List of UIDs (plain text)</option> - <option value="null-text">text ASN.1</option> - <option value="null-asn.1">binary ASN.1</option> - <option value="native-xml">Full record in XML</option> - <option value="acc-text">Accession number(s)</option> - <option value="fasta-text">FASTA</option> - <option value="fasta-xml">TinySeq XML</option> - <option value="seqid-text">SeqID string</option> - <option value="ft-text">Feature table</option> - <option value="gp-text">GenPept flat file</option> - <option value="gp-xml">GBSeq XML</option> - <option value="gpc-xml">INSDSeq XML</option> - <option value="ipg-xml">Identical Protein XML</option> + <option value="docsum-json">Document Summary (json)</option> + <option value="docsum-xml">Document Summary (xml)</option> + <option value="full-text">Full Document (text)</option> + <option value="full-xml">Full Document (xml)</option> + <option value="uilist-text">Unique Identifier List (text)</option> + <option value="uilist-xml">Unique Identifier List (xml)</option> </param> </when> <when value="proteinclusters"> <param name="output_format" type="select" label="Output Format"> - <option value="docsum-xml">Document summary</option> - <option value="uilist-xml">List of UIDs (XML)</option> - <option value="uilist-text">List of UIDs (plain text)</option> + <option value="docsum-json">Document Summary (json)</option> + <option value="docsum-xml">Document Summary (xml)</option> + <option value="full-text">Full Document (text)</option> + <option value="full-xml">Full Document (xml)</option> + <option value="uilist-text">Unique Identifier List (text)</option> + <option value="uilist-xml">Unique Identifier List (xml)</option> </param> </when> <when value="pubmed"> <param name="output_format" type="select" label="Output Format"> - <option value="docsum-xml">Document summary</option> - <option value="uilist-xml">List of UIDs (XML)</option> - <option value="uilist-text">List of UIDs (plain text)</option> - <option value="null-asn.1">text ASN.1</option> - <option value="null-xml">XML</option> - <option value="medline-text">MEDLINE</option> - <option value="uilist-text">PMID list</option> - <option value="abstract-text">Abstract</option> + <option value="abstract-xml">Abstract (xml)</option> + <option value="docsum-json">Document Summary (json)</option> + <option value="docsum-xml">Document Summary (xml)</option> + <option value="full-text">Full Document (text)</option> + <option value="full-xml">Full Document (xml)</option> + <option value="medline-text">MEDLINE (text)</option> + <option value="native-asn.1">Pubmed-entry (asn.1)</option> + <option value="native-xml">PubmedArticleSet (xml)</option> + <option value="uilist-text">Unique Identifier List (text)</option> + <option value="uilist-xml">Unique Identifier List (xml)</option> </param> </when> <when value="pubmedhealth"> <param name="output_format" type="select" label="Output Format"> - <option value="docsum-xml">Document summary</option> - <option value="uilist-xml">List of UIDs (XML)</option> - <option value="uilist-text">List of UIDs (plain text)</option> + <option value="docsum-json">Document Summary (json)</option> + <option value="docsum-xml">Document Summary (xml)</option> + <option value="full-text">Full Document (text)</option> + <option value="full-xml">Full Document (xml)</option> + <option value="uilist-text">Unique Identifier List (text)</option> + <option value="uilist-xml">Unique Identifier List (xml)</option> + </param> + </when> + <when value="seqannot"> + <param name="output_format" type="select" label="Output Format"> + <option value="docsum-json">Document Summary (json)</option> + <option value="docsum-xml">Document Summary (xml)</option> + <option value="full-text">Full Document (text)</option> + <option value="full-xml">Full Document (xml)</option> + <option value="uilist-text">Unique Identifier List (text)</option> + <option value="uilist-xml">Unique Identifier List (xml)</option> </param> </when> <when value="snp"> <param name="output_format" type="select" label="Output Format"> - <option value="docsum-xml">Document summary</option> - <option value="uilist-xml">List of UIDs (XML)</option> - <option value="uilist-text">List of UIDs (plain text)</option> - <option value="null-asn.1">text ASN.1</option> - <option value="null-xml">XML</option> - <option value="flt-text">Flat file</option> - <option value="fasta-text">FASTA</option> - <option value="rsr-text">RS Cluster report</option> - <option value="ssexemplar-text">SS Exemplar list</option> - <option value="chr-text">Chromosome report</option> - <option value="docset-text">Summary</option> - <option value="uilist-xml">UID list (XML)</option> - <option value="uilist-text">UID list (text)</option> + <option value="chr-text">Chromosome Report (text)</option> + <option value="docset-text">Summary (text)</option> + <option value="docsum-json">Document Summary (json)</option> + <option value="docsum-xml">Document Summary (xml)</option> + <option value="fasta-fasta">FASTA (fasta)</option> + <option value="flt-text">Flat File (text)</option> + <option value="full-text">Full Document (text)</option> + <option value="full-xml">Full Document (xml)</option> + <option value="native-asn.1">Rs (asn.1)</option> + <option value="native-xml">ExchangeSet (xml)</option> + <option value="rsr-tabular">RS Cluster Report (tabular)</option> + <option value="ssexemplar-text">SS Exemplar List (text)</option> + <option value="uilist-text">Unique Identifier List (text)</option> + <option value="uilist-xml">Unique Identifier List (xml)</option> </param> </when> <when value="sra"> <param name="output_format" type="select" label="Output Format"> - <option value="docsum-xml">Document summary</option> - <option value="uilist-xml">List of UIDs (XML)</option> - <option value="uilist-text">List of UIDs (plain text)</option> - <option value="full-xml">XML</option> + <option value="docsum-json">Document Summary (json)</option> + <option value="docsum-xml">Document Summary (xml)</option> + <option value="full-text">Full Document (text)</option> + <option value="full-xml">Full Document (xml)</option> + <option value="native-xml">EXPERIMENT_PACKAGE_SET (xml)</option> + <option value="runinfo-xml">SraRunInfo (xml)</option> + <option value="uilist-text">Unique Identifier List (text)</option> + <option value="uilist-xml">Unique Identifier List (xml)</option> </param> </when> <when value="structure"> <param name="output_format" type="select" label="Output Format"> - <option value="docsum-xml">Document summary</option> - <option value="uilist-xml">List of UIDs (XML)</option> - <option value="uilist-text">List of UIDs (plain text)</option> + <option value="docsum-json">Document Summary (json)</option> + <option value="docsum-xml">Document Summary (xml)</option> + <option value="full-text">Full Document (text)</option> + <option value="full-xml">Full Document (xml)</option> + <option value="mmdb-asn.1">Ncbi-mime-asn1 strucseq (asn.1)</option> + <option value="native-text">MMDB Report (text)</option> + <option value="native-xml">RecordSet (xml)</option> + <option value="uilist-text">Unique Identifier List (text)</option> + <option value="uilist-xml">Unique Identifier List (xml)</option> </param> </when> <when value="taxonomy"> <param name="output_format" type="select" label="Output Format"> - <option value="docsum-xml">Document summary</option> - <option value="uilist-xml">List of UIDs (XML)</option> - <option value="uilist-text">List of UIDs (plain text)</option> - <option value="null-xml">XML</option> - <option value="uilist-xml">TaxID list (XML)</option> - <option value="uilist-text">TaxID list (text)</option> + <option value="docsum-json">Document Summary (json)</option> + <option value="docsum-xml">Document Summary (xml)</option> + <option value="full-text">Full Document (text)</option> + <option value="full-xml">Full Document (xml)</option> + <option value="native-text">Taxonomy List (text)</option> + <option value="native-xml">TaxaSet (xml)</option> + <option value="uilist-text">Unique Identifier List (text)</option> + <option value="uilist-xml">Unique Identifier List (xml)</option> + </param> + </when> + <when value="unigene"> + <param name="output_format" type="select" label="Output Format"> + <option value="docsum-json">Document Summary (json)</option> + <option value="docsum-xml">Document Summary (xml)</option> + <option value="full-text">Full Document (text)</option> + <option value="full-xml">Full Document (xml)</option> + <option value="uilist-text">Unique Identifier List (text)</option> + <option value="uilist-xml">Unique Identifier List (xml)</option> </param> </when> </conditional> </xml> + + <xml name="efetch_formats"> + <change_format> + <when input="output_format" value="fasta_cds_na-fasta" format="fasta"/> + <when input="output_format" value="ipg-xml" format="xml"/> + <when input="output_format" value="gbc-xml" format="xml"/> + <when input="output_format" value="medline-text" format="text"/> + <when input="output_format" value="native-None" format="text"/> + <when input="output_format" value="mmdb-asn.1" format="asn1"/> + <when input="output_format" value="seqid-asn.1" format="asn1"/> + <when input="output_format" value="acc-text" format="text"/> + <when input="output_format" value="summary-text" format="text"/> + <when input="output_format" value="gene_fasta-fasta" format="fasta"/> + <when input="output_format" value="native-text" format="text"/> + <when input="output_format" value="gbwithparts-text" format="text"/> + <when input="output_format" value="gpc-xml" format="xml"/> + <when input="output_format" value="fasta_cds_aa-fasta" format="fasta"/> + <when input="output_format" value="gp-text" format="text"/> + <when input="output_format" value="gss-text" format="text"/> + <when input="output_format" value="ipg-text" format="text"/> + <when input="output_format" value="uilist-xml" format="xml"/> + <when input="output_format" value="docsum-xml" format="xml"/> + <when input="output_format" value="rsr-tabular" format="tabular"/> + <when input="output_format" value="uilist-text" format="text"/> + <when input="output_format" value="gb-text" format="text"/> + <when input="output_format" value="chr-text" format="text"/> + <when input="output_format" value="alignmentscores-text" format="text"/> + <when input="output_format" value="native-asn.1" format="asn1"/> + <when input="output_format" value="gp-xml" format="xml"/> + <when input="output_format" value="tabular-tabular" format="tabular"/> + <when input="output_format" value="ssexemplar-text" format="text"/> + <when input="output_format" value="docsum-json" format="json"/> + <when input="output_format" value="fasta-xml" format="xml"/> + <when input="output_format" value="runinfo-xml" format="xml"/> + <when input="output_format" value="flt-text" format="text"/> + <when input="output_format" value="fasta-fasta" format="fasta"/> + <when input="output_format" value="full-text" format="text"/> + <when input="output_format" value="gb-xml" format="xml"/> + <when input="output_format" value="abstract-xml" format="xml"/> + <when input="output_format" value="full-xml" format="xml"/> + <when input="output_format" value="ft-text" format="text"/> + <when input="output_format" value="homologene-text" format="text"/> + <when input="output_format" value="est-xml" format="xml"/> + <when input="output_format" value="gene_table-xml" format="xml"/> + <when input="output_format" value="docset-text" format="text"/> + <when input="output_format" value="native-xml" format="xml"/> + </change_format> + </xml> <token name="@LIST_OR_HIST@"> #if $query_source.qss == "history": --history_file $query_source.history_file @@ -576,5 +842,5 @@ <param name="linkname" type="select" label="To NCBI Database"> <!-- TODO: http://eutils.ncbi.nlm.nih.gov/entrez/query/static/entrezlinks.html --> </param> -</xml> + </xml> </macros>