Mercurial > repos > iuc > ncbi_eutils_esearch
diff macros.xml @ 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 | 02c7d63c7240 |
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--- 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>