Mercurial > repos > iuc > ncbi_eutils_esearch
diff macros.xml @ 3:e267701c187b draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
| author | iuc |
|---|---|
| date | Wed, 23 Sep 2020 09:48:26 +0000 |
| parents | c6096cd97120 |
| children | 67602de82f6e |
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--- a/macros.xml Wed Mar 11 04:03:14 2020 -0400 +++ b/macros.xml Wed Sep 23 09:48:26 2020 +0000 @@ -1,7 +1,7 @@ <?xml version="1.0"?> <macros> <token name="@PROFILE@">18.01</token> - <token name="@WRAPPER_VERSION@">1.3</token> + <token name="@WRAPPER_VERSION@">1.70</token> <token name="@EMAIL_ARGUMENTS@"> --user_email "$__user_email__" #set admin_emails = ';'.join(str($__admin_users__).split(',')) @@ -86,743 +86,51 @@ and licensing restrictions of linked pages and to secure all necessary permissions. ]]></token> - <xml name="dbselect" - token_name="db_select" - 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> - <option value="biosystems">Biosystems</option> - <option value="blastdbinfo">Blast Database Information</option> - <option value="books">Books</option> - <option value="cdd">Conserved Domains</option> - <option value="clinvar">Clinical Variants</option> - <option value="clone">CLone</option> - <option value="dbvar">dbVar</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="medgen">MedGen</option> - <option value="mesh">MeSH</option> - <option value="ncbisearch">NCBI Web Site</option> - <option value="nlmcatalog">NLM Catalog</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> - <option value="pmc">PubMed Central</option> - <option value="popset">PopSet</option> - <option value="probe">Probe</option> - <option value="protein">Protein</option> - <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="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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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-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="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-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-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-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-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="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="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="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-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-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-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-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-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-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-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-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-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="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-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="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-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-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-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": +#if $query_source.qss == "history_json": --history_file $query_source.history_file +#else if $query_source.qss == "history_xml": + --history_xml $query_source.history_xml #else if $query_source.qss == "id_file": --id_list $query_source.id_file #else if $query_source.qss == "id_list": --id $query_source.id_list +#else if $query_source.qss == "id_xml": + --id_xml $query_source.id_xml +#else if $query_source.qss == "id_json": + --id_json $query_source.id_json #end if - </token> + </token> <xml name="list_or_hist"> <conditional name="query_source"> - <param name="qss" type="select" label="Select source for IDs"> - <option value="history">NCBI WebEnv History</option> - <option value="id_file">File containing IDs (one per line)</option> - <option value="id_list">Direct Entry</option> + <param name="qss" type="select" label="Enter Query IDs by..." help="Files output by ELink or ESearch are acceptable. Query IDs in an ELink result are ignored."> + <option value="history_json">History File (JSON)</option> + <option value="history_xml">History File (XML)</option> + <option value="id_file" selected="True">ID file (Tabular)</option> + <option value="id_xml">ID File (XML)</option> + <option value="id_json">ID File (JSON)</option> + <option value="id_list">Paste IDs</option> </param> - <when value="history"> - <param label="History File" name="history_file" type="data" format="json"/> + <when value="history_json"> + <param label="History File (JSON)" name="history_file" type="data" format="json" help="A JSON file containing the WebEnv ID and Query Key referencing the search on the NCBI history server"/> + </when> + <when value="history_xml"> + <param label="History File (XML)" name="history_xml" type="data" format="xml" help="An XML file containing the WebEnv ID and Query Key referencing the search on the NCBI history server"/> </when> <when value="id_file"> - <param label="ID List" name="id_file" type="data" format="text,tabular"/> + <param label="ID File (Text)" name="id_file" type="data" format="text,tabular" help="A Text file containing one ID per line"/> + </when> + <when value="id_xml"> + <param label="ID File (XML)" name="id_xml" type="data" format="xml" help="ESearch or ELink Result XML file"/> + </when> + <when value="id_json"> + <param label="ID File (JSON)" name="id_json" type="data" format="json" help="ESearch or ELink Result JSON file"/> </when> <when value="id_list"> - <param label="ID List" name="id_list" type="text" area="true" help="Newline/Comma separated list of IDs"/> + <param label="Paste ID List" name="id_list" type="text" area="true" help="Newline/Comma separated list of IDs"/> </when> </conditional> </xml> - <xml name="history_out"> - <data format="json" name="history" label="NCBI Entrez WebEnv History"> - <yield/> - </data> - </xml> <xml name="citations"> <citations> <citation type="bibtex">@Book{ncbiEutils, @@ -836,12 +144,4400 @@ </xml> <xml name="requirements"> <requirements> + <requirement type="package" version="3">python</requirement> <requirement type="package" version="1.70">biopython</requirement> </requirements> </xml> - <xml name="linkname"> - <param name="linkname" type="select" label="To NCBI Database"> - <!-- TODO: https://eutils.ncbi.nlm.nih.gov/entrez/query/static/entrezlinks.html --> + <token name="@EFETCH_FORMAT_TOKEN@"> + <![CDATA[ + + ## This token must go at the end of the efetch command + + #set rettype, retmode, format = str($db.output_format).split('-') + + #if retmode != "none": + --retmode $retmode + #end if + ## Otherwise, defaults to a None/empty which implies 'default' to NCBI + + #if rettype != "none": + --rettype $rettype + #end if + + --galaxy_format $format + + ]]> + </token> + <xml name="dbselect_efetch" token_name="db_select" token_label="NCBI Database to Query"> + <param name="@NAME@" type="select" label="@LABEL@"> + <option value="bioproject">BioProject (bioproject)</option> + <option value="biosample">BioSample (biosample)</option> + <option value="biosystems">BioSystems (biosystems)</option> + <option value="clinvar">ClinVar (clinvar)</option> + <option value="gds">GEO DataSets (gds)</option> + <option value="gtr">GTR (gtr)</option> + <option value="gene">Gene (gene)</option> + <option value="homologene">HomoloGene (homologene)</option> + <option value="mesh">MeSH (mesh)</option> + <option value="nlmcatalog">NLM Catalog (nlmcatalog)</option> + <option value="nuccore">Nucleotide (nuccore)</option> + <option value="pmc">PMC (pmc)</option> + <option value="popset">PopSet (popset)</option> + <option value="protein">Protein (protein)</option> + <option value="pubmed" selected="True">PubMed (pubmed)</option> + <option value="snp">SNP (snp)</option> + <option value="sra">SRA (sra)</option> + <option value="taxonomy">Taxonomy (taxonomy)</option> + </param> + </xml> + <xml name="efetchdb"> + <conditional name="db"> + <expand macro="dbselect_efetch" /> + <when value="bioproject"> + <param name="output_format" type="select" label="Output Format"> + <option value="docsum-xml-xml">Document summary (xml)</option> + <option value="xml-xml-xml">Full record (xml)</option> + <option value="uilist-text-tabular">List of UIDs (tabular)</option> + <option value="uilist-xml-xml">List of UIDs (xml)</option> + </param> + </when> + <when value="biosample"> + <param name="output_format" type="select" label="Output Format"> + <option value="docsum-xml-xml">Document summary (xml)</option> + <option value="full-text-txt">Full record (txt)</option> + <option value="full-xml-xml">Full record (xml)</option> + <option value="uilist-text-tabular">List of UIDs (tabular)</option> + <option value="uilist-xml-xml">List of UIDs (xml)</option> + </param> + </when> + <when value="biosystems"> + <param name="output_format" type="select" label="Output Format"> + <option value="docsum-xml-xml">Document summary (xml)</option> + <option value="xml-xml-xml">Full record (xml)</option> + <option value="uilist-text-tabular">List of UIDs (tabular)</option> + <option value="uilist-xml-xml">List of UIDs (xml)</option> + </param> + </when> + <when value="clinvar"> + <param name="output_format" type="select" label="Output Format"> + <option value="clinvarset-xml-xml">ClinVar Set (xml)</option> + <option value="docsum-xml-xml">Document summary (xml)</option> + <option value="none-none-xml">Full (xml)</option> + <option value="uilist-text-tabular">List of UIDs (tabular)</option> + <option value="uilist-xml-xml">List of UIDs (xml)</option> + </param> + </when> + <when value="gds"> + <param name="output_format" type="select" label="Output Format"> + <option value="docsum-xml-xml">Document summary (xml)</option> + <option value="none-none-xml">Full (xml)</option> + <option value="uilist-text-tabular">List of UIDs (tabular)</option> + <option value="uilist-xml-xml">List of UIDs (xml)</option> + <option value="summary-text-txt">Summary (txt)</option> + </param> + </when> + <when value="gtr"> + <param name="output_format" type="select" label="Output Format"> + <option value="docsum-xml-xml">Document summary (xml)</option> + <option value="none-none-xml">Full (xml)</option> + <option value="gtracc-xml-xml">GTR Test Report (xml)</option> + <option value="uilist-text-tabular">List of UIDs (tabular)</option> + <option value="uilist-xml-xml">List of UIDs (xml)</option> + </param> + </when> + <when value="gene"> + <param name="output_format" type="select" label="Output Format"> + <option value="docsum-xml-xml">Document summary (xml)</option> + <option value="none-xml-xml">Full (xml)</option> + <option value="gene_table-text-txt">Gene table (txt)</option> + <option value="uilist-text-tabular">List of UIDs (tabular)</option> + <option value="uilist-xml-xml">List of UIDs (xml)</option> + <option value="none-asn.1-txt">text ASN.1 (txt)</option> + </param> + </when> + <when value="homologene"> + <param name="output_format" type="select" label="Output Format"> + <option value="alignmentscores-text-tabular">Alignment scores (tabular)</option> + <option value="docsum-xml-xml">Document summary (xml)</option> + <option value="fasta-text-fasta">FASTA (fasta)</option> + <option value="none-xml-xml">Full (xml)</option> + <option value="homologene-text-txt">HomoloGene (txt)</option> + <option value="uilist-text-tabular">List of UIDs (tabular)</option> + <option value="uilist-xml-xml">List of UIDs (xml)</option> + <option value="none-asn.1-txt">text ASN.1 (txt)</option> + </param> + </when> + <when value="mesh"> + <param name="output_format" type="select" label="Output Format"> + <option value="docsum-xml-xml">Document summary (xml)</option> + <option value="full-text-txt">Full record (txt)</option> + <option value="uilist-text-tabular">List of UIDs (tabular)</option> + <option value="uilist-xml-xml">List of UIDs (xml)</option> + </param> + </when> + <when value="nlmcatalog"> + <param name="output_format" type="select" label="Output Format"> + <option value="docsum-xml-xml">Document summary (xml)</option> + <option value="none-xml-xml">Full (xml)</option> + <option value="none-text-txt">Full record (txt)</option> + <option value="uilist-text-tabular">List of UIDs (tabular)</option> + <option value="uilist-xml-xml">List of UIDs (xml)</option> + </param> + </when> + <when value="nuccore"> + <param name="output_format" type="select" label="Output Format"> + <option value="acc-text-tabular">Accession number(s) (tabular)</option> + <option value="fasta_cds_na-text-fasta">CDS nucleotide FASTA (fasta)</option> + <option value="fasta_cds_aa-text-fasta">CDS protein FASTA (fasta)</option> + <option value="docsum-xml-xml">Document summary (xml)</option> + <option value="fasta-text-fasta">FASTA (fasta)</option> + <option value="ft-text-txt">Feature table (txt)</option> + <option value="native-xml-xml">Full record (xml)</option> + <option value="gb-xml-xml">GBSeq (xml)</option> + <option value="gb-text-genbank">GenBank flat file (genbank)</option> + <option value="gbwithparts-text-genbank">GenBank flat file with full sequence (contigs) (genbank)</option> + <option value="gbc-xml-xml">INSDSeq (xml)</option> + <option value="uilist-text-tabular">List of UIDs (tabular)</option> + <option value="uilist-xml-xml">List of UIDs (xml)</option> + <option value="seqid-text-tabular">SeqID string (tabular)</option> + <option value="fasta-xml-xml">TinySeq (xml)</option> + <option value="none-asn.1-binary">binary ASN.1 (binary)</option> + <option value="none-text-txt">text ASN.1 (txt)</option> + </param> + </when> + <when value="pmc"> + <param name="output_format" type="select" label="Output Format"> + <option value="docsum-xml-xml">Document summary (xml)</option> + <option value="none-xml-xml">FULL (xml)</option> + <option value="uilist-text-tabular">List of UIDs (tabular)</option> + <option value="uilist-xml-xml">List of UIDs (xml)</option> + <option value="medline-text-txt">MEDLINE (txt)</option> + </param> + </when> + <when value="popset"> + <param name="output_format" type="select" label="Output Format"> + <option value="acc-text-tabular">Accession number(s) (tabular)</option> + <option value="docsum-xml-xml">Document summary (xml)</option> + <option value="fasta-text-fasta">FASTA (fasta)</option> + <option value="native-xml-xml">Full record (xml)</option> + <option value="gb-xml-xml">GBSeq (xml)</option> + <option value="gb-text-genbank">GenBank flat file (genbank)</option> + <option value="gbc-xml-xml">INSDSeq (xml)</option> + <option value="uilist-text-tabular">List of UIDs (tabular)</option> + <option value="uilist-xml-xml">List of UIDs (xml)</option> + <option value="seqid-text-tabular">SeqID string (tabular)</option> + <option value="fasta-xml-xml">TinySeq (xml)</option> + <option value="none-asn.1-binary">binary ASN.1 (binary)</option> + <option value="none-text-txt">text ASN.1 (txt)</option> + </param> + </when> + <when value="protein"> + <param name="output_format" type="select" label="Output Format"> + <option value="acc-text-tabular">Accession number(s) (tabular)</option> + <option value="docsum-xml-xml">Document summary (xml)</option> + <option value="fasta-text-fasta">FASTA (fasta)</option> + <option value="ft-text-txt">Feature table (txt)</option> + <option value="native-xml-xml">Full record (xml)</option> + <option value="gp-xml-xml">GBSeq (xml)</option> + <option value="gp-text-txt">GenPept flat file (txt)</option> + <option value="gpc-xml-xml">INSDSeq (xml)</option> + <option value="ipg-xml-xml">Identical Protein (xml)</option> + <option value="uilist-text-tabular">List of UIDs (tabular)</option> + <option value="uilist-xml-xml">List of UIDs (xml)</option> + <option value="seqid-text-tabular">SeqID string (tabular)</option> + <option value="fasta-xml-xml">TinySeq (xml)</option> + <option value="none-asn.1-binary">binary ASN.1 (binary)</option> + <option value="none-text-txt">text ASN.1 (txt)</option> + </param> + </when> + <when value="pubmed"> + <param name="output_format" type="select" label="Output Format"> + <option value="abstract-text-txt">Abstract (txt)</option> + <option value="docsum-xml-xml">Document summary (xml)</option> + <option value="none-xml-xml">Full (xml)</option> + <option value="uilist-text-tabular">List of UIDs (tabular)</option> + <option value="uilist-xml-xml">List of UIDs (xml)</option> + <option value="medline-text-txt">MEDLINE (txt)</option> + <option value="none-asn.1-txt">text ASN.1 (txt)</option> + </param> + </when> + <when value="snp"> + <param name="output_format" type="select" label="Output Format"> + <option value="chr-text-txt">Chromosome report (txt)</option> + <option value="docsum-json-json">Document summary (json)</option> + <option value="docsum-xml-xml">Document summary (xml)</option> + <option value="fasta-text-fasta">FASTA (fasta)</option> + <option value="flt-text-txt">Flat file (txt)</option> + <option value="uilist-json-json">List of UIDs (json)</option> + <option value="uilist-text-tabular">List of UIDs (tabular)</option> + <option value="uilist-xml-xml">List of UIDs (xml)</option> + <option value="rsr-text-txt">RS Cluster report (txt)</option> + <option value="ssexemplar-text-tabular">SS Exemplar list (tabular)</option> + <option value="docset-text-txt">Summary (txt)</option> + <option value="none-xml-xml">XML (xml)</option> + <option value="none-asn.1-txt">text ASN.1 (txt)</option> + </param> + </when> + <when value="sra"> + <param name="output_format" type="select" label="Output Format"> + <option value="docsum-xml-xml">Document summary (xml)</option> + <option value="full-xml-xml">Full (xml)</option> + <option value="uilist-text-tabular">List of UIDs (tabular)</option> + </param> + </when> + <when value="taxonomy"> + <param name="output_format" type="select" label="Output Format"> + <option value="docsum-xml-xml">Document summary (xml)</option> + <option value="none-xml-xml">Full (xml)</option> + <option value="uilist-text-tabular">List of UIDs (tabular)</option> + <option value="uilist-xml-xml">List of UIDs (xml)</option> + </param> + </when> + </conditional> + </xml> + <xml name="dbselect" token_name="db_select" token_label="NCBI Database to Query"> + <param name="@NAME@" type="select" label="@LABEL@"> + <option value="annotinfo">AnnotInfo (annotinfo)</option> + <option value="assembly">Assembly (assembly)</option> + <option value="bioproject">BioProject (bioproject)</option> + <option value="biosample">BioSample (biosample)</option> + <option value="biosystems">BioSystems (biosystems)</option> + <option value="biocollections">Biocollections (biocollections)</option> + <option value="blastdbinfo">BlastdbInfo (blastdbinfo)</option> + <option value="books">Books (books)</option> + <option value="clinvar">ClinVar (clinvar)</option> + <option value="cdd">Conserved Domains (cdd)</option> + <option value="gds">GEO DataSets (gds)</option> + <option value="geoprofiles">GEO Profiles (geoprofiles)</option> + <option value="gtr">GTR (gtr)</option> + <option value="gapplus">GaPPlus (gapplus)</option> + <option value="gene">Gene (gene)</option> + <option value="genome">Genome (genome)</option> + <option value="homologene">HomoloGene (homologene)</option> + <option value="ipg">Identical Protein Groups (ipg)</option> + <option value="mesh">MeSH (mesh)</option> + <option value="medgen">MedGen (medgen)</option> + <option value="ncbisearch">NCBI Web Site (ncbisearch)</option> + <option value="nlmcatalog">NLM Catalog (nlmcatalog)</option> + <option value="nuccore">Nucleotide (nuccore)</option> + <option value="nucleotide">Nucleotide (nucleotide)</option> + <option value="omim">OMIM (omim)</option> + <option value="orgtrack">Orgtrack (orgtrack)</option> + <option value="pmc">PMC (pmc)</option> + <option value="popset">PopSet (popset)</option> + <option value="protein">Protein (protein)</option> + <option value="proteinclusters">Protein Clusters (proteinclusters)</option> + <option value="pcassay">PubChem BioAssay (pcassay)</option> + <option value="pccompound">PubChem Compound (pccompound)</option> + <option value="pcsubstance">PubChem Substance (pcsubstance)</option> + <option value="pubmed">PubMed (pubmed)</option> + <option value="snp">SNP (snp)</option> + <option value="sra">SRA (sra)</option> + <option value="seqannot">SeqAnnot (seqannot)</option> + <option value="sparcle">Sparcle (sparcle)</option> + <option value="structure">Structure (structure)</option> + <option value="taxonomy">Taxonomy (taxonomy)</option> + <option value="gap">dbGaP (gap)</option> + <option value="dbvar">dbVar (dbvar)</option> + <option value="grasp">grasp (grasp)</option> + </param> + </xml> + <xml name="dbselect_linked" token_name="db_select_linked" token_label="NCBI Database to Use"> + <param name="@NAME@" type="select" label="@LABEL@"> + <option value="annotinfo">AnnotInfo (annotinfo)</option> + <option value="assembly">Assembly (assembly)</option> + <option value="bioproject">BioProject (bioproject)</option> + <option value="biosample">BioSample (biosample)</option> + <option value="biosystems">BioSystems (biosystems)</option> + <option value="biocollections">Biocollections (biocollections)</option> + <option value="blastdbinfo">BlastdbInfo (blastdbinfo)</option> + <option value="books">Books (books)</option> + <option value="clinvar">ClinVar (clinvar)</option> + <option value="cdd">Conserved Domains (cdd)</option> + <option value="gds">GEO DataSets (gds)</option> + <option value="geoprofiles">GEO Profiles (geoprofiles)</option> + <option value="gtr">GTR (gtr)</option> + <option value="gapplus">GaPPlus (gapplus)</option> + <option value="gene">Gene (gene)</option> + <option value="genome">Genome (genome)</option> + <option value="homologene">HomoloGene (homologene)</option> + <option value="ipg">Identical Protein Groups (ipg)</option> + <option value="mesh">MeSH (mesh)</option> + <option value="medgen">MedGen (medgen)</option> + <option value="ncbisearch">NCBI Web Site (ncbisearch)</option> + <option value="nlmcatalog">NLM Catalog (nlmcatalog)</option> + <option value="nuccore">Nucleotide (nuccore)</option> + <option value="nucleotide">Nucleotide (nucleotide)</option> + <option value="omim">OMIM (omim)</option> + <option value="orgtrack">Orgtrack (orgtrack)</option> + <option value="pmc">PMC (pmc)</option> + <option value="popset">PopSet (popset)</option> + <option value="protein">Protein (protein)</option> + <option value="proteinclusters">Protein Clusters (proteinclusters)</option> + <option value="pcassay">PubChem BioAssay (pcassay)</option> + <option value="pccompound">PubChem Compound (pccompound)</option> + <option value="pcsubstance">PubChem Substance (pcsubstance)</option> + <option value="pubmed">PubMed (pubmed)</option> + <option value="snp">SNP (snp)</option> + <option value="sra">SRA (sra)</option> + <option value="seqannot">SeqAnnot (seqannot)</option> + <option value="sparcle">Sparcle (sparcle)</option> + <option value="structure">Structure (structure)</option> + <option value="taxonomy">Taxonomy (taxonomy)</option> + <option value="gap">dbGaP (gap)</option> + <option value="dbvar">dbVar (dbvar)</option> + <option value="grasp">grasp (grasp)</option> </param> </xml> + <xml name="none_link_macro"> + <conditional name="db_to"> + <param name="db_select_to" type="select" label="To NCBI Database (n/a)"> + <option value="n/a">Not applicable</option> + </param> + <when value="n/a"> + <param name="linkname" type="select" label="Link Name (n/a)"> + <option value="n/a">Not applicable</option> + </param> + </when> + </conditional> + </xml> + <xml name="db_link_macro"> + <conditional name="db_from_link"> + <expand macro="dbselect_linked" name="db_select_from_link" label="From NCBI Database" /> + <when value="annotinfo"> + <expand macro="none_link_macro" name="db_select_none" label="To NCBI Database" /> + </when> + <when value="assembly"> + <expand macro="none_link_macro" name="db_select_none" label="To NCBI Database" /> + </when> + <when value="bioproject"> + <expand macro="none_link_macro" name="db_select_none" label="To NCBI Database" /> + </when> + <when value="biosample"> + <expand macro="none_link_macro" name="db_select_none" label="To NCBI Database" /> + </when> + <when value="biosystems"> + <expand macro="none_link_macro" name="db_select_none" label="To NCBI Database" /> + </when> + <when value="biocollections"> + <expand macro="none_link_macro" name="db_select_none" label="To NCBI Database" /> + </when> + <when value="blastdbinfo"> + <expand macro="none_link_macro" name="db_select_none" label="To NCBI Database" /> + </when> + <when value="books"> + <expand macro="none_link_macro" name="db_select_none" label="To NCBI Database" /> + </when> + <when value="clinvar"> + <expand macro="none_link_macro" name="db_select_none" label="To NCBI Database" /> + </when> + <when value="cdd"> + <expand macro="none_link_macro" name="db_select_none" label="To NCBI Database" /> + </when> + <when value="gds"> + <expand macro="none_link_macro" name="db_select_none" label="To NCBI Database" /> + </when> + <when value="geoprofiles"> + <expand macro="none_link_macro" name="db_select_none" label="To NCBI Database" /> + </when> + <when value="gtr"> + <expand macro="none_link_macro" name="db_select_none" label="To NCBI Database" /> + </when> + <when value="gapplus"> + <expand macro="none_link_macro" name="db_select_none" label="To NCBI Database" /> + </when> + <when value="gene"> + <expand macro="none_link_macro" name="db_select_none" label="To NCBI Database" /> + </when> + <when value="genome"> + <expand macro="none_link_macro" name="db_select_none" label="To NCBI Database" /> + </when> + <when value="homologene"> + <expand macro="none_link_macro" name="db_select_none" label="To NCBI Database" /> + </when> + <when value="ipg"> + <expand macro="none_link_macro" name="db_select_none" label="To NCBI Database" /> + </when> + <when value="mesh"> + <expand macro="none_link_macro" name="db_select_none" label="To NCBI Database" /> + </when> + <when value="medgen"> + <expand macro="none_link_macro" name="db_select_none" label="To NCBI Database" /> + </when> + <when value="ncbisearch"> + <expand macro="none_link_macro" name="db_select_none" label="To NCBI Database" /> + </when> + <when value="nlmcatalog"> + <expand macro="none_link_macro" name="db_select_none" label="To NCBI Database" /> + </when> + <when value="nuccore"> + <expand macro="none_link_macro" name="db_select_none" label="To NCBI Database" /> + </when> + <when value="nucleotide"> + <expand macro="none_link_macro" name="db_select_none" label="To NCBI Database" /> + </when> + <when value="omim"> + <expand macro="none_link_macro" name="db_select_none" label="To NCBI Database" /> + </when> + <when value="orgtrack"> + <expand macro="none_link_macro" name="db_select_none" label="To NCBI Database" /> + </when> + <when value="pmc"> + <expand macro="none_link_macro" name="db_select_none" label="To NCBI Database" /> + </when> + <when value="popset"> + <expand macro="none_link_macro" name="db_select_none" label="To NCBI Database" /> + </when> + <when value="protein"> + <expand macro="none_link_macro" name="db_select_none" label="To NCBI Database" /> + </when> + <when value="proteinclusters"> + <expand macro="none_link_macro" name="db_select_none" label="To NCBI Database" /> + </when> + <when value="pcassay"> + <expand macro="none_link_macro" name="db_select_none" label="To NCBI Database" /> + </when> + <when value="pccompound"> + <expand macro="none_link_macro" name="db_select_none" label="To NCBI Database" /> + </when> + <when value="pcsubstance"> + <expand macro="none_link_macro" name="db_select_none" label="To NCBI Database" /> + </when> + <when value="pubmed"> + <expand macro="none_link_macro" name="db_select_none" label="To NCBI Database" /> + </when> + <when value="snp"> + <expand macro="none_link_macro" name="db_select_none" label="To NCBI Database" /> + </when> + <when value="sra"> + <expand macro="none_link_macro" name="db_select_none" label="To NCBI Database" /> + </when> + <when value="seqannot"> + <expand macro="none_link_macro" name="db_select_none" label="To NCBI Database" /> + </when> + <when value="sparcle"> + <expand macro="none_link_macro" name="db_select_none" label="To NCBI Database" /> + </when> + <when value="structure"> + <expand macro="none_link_macro" name="db_select_none" label="To NCBI Database" /> + </when> + <when value="taxonomy"> + <expand macro="none_link_macro" name="db_select_none" label="To NCBI Database" /> + </when> + <when value="gap"> + <expand macro="none_link_macro" name="db_select_none" label="To NCBI Database" /> + </when> + <when value="dbvar"> + <expand macro="none_link_macro" name="db_select_none" label="To NCBI Database" /> + </when> + <when value="grasp"> + <expand macro="none_link_macro" name="db_select_none" label="To NCBI Database" /> + </when> + </conditional> + </xml> + <xml name="linkmacro"> + <conditional name="cmd"> + <param name="cmd_select" type="select" label="Link Method" help="Fetch UIDs from the 'To' Database that are linked to supplied UIDs in the 'From' database"> + <option value="neighbor" selected="true">Neighbor (neighbor)</option> + <option value="neighbor_history">Neighbor, save result in history server (neighbor_history)</option> + <option value="neighbor_score">Neighbor Score (neighbor_score)</option> + <option value="acheck">Show available links to any database (acheck)</option> + <option value="ncheck">Show available links within the same database (ncheck)</option> + <option value="lcheck">Show available links to external sources (LinkOuts) (lcheck)</option> + <option value="llinks">Show available URLs and attributes for non-library LinkOut providers (llinks)</option> + <option value="llinkslib">Show available URLs and attributes for all LinkOut Providers (llinkslib)</option> + <option value="prlinks">Show available primary LinkOut Provider Links (prlinks)</option> + </param> + <when value="neighbor"> + <expand macro="db_db_link_macro" name="link_select" label="Link name" /> + <param name="output_format" type="select" label="Output Format"> + <option value="xml">ID File (xml)</option> + <option value="json">ID File (json)</option> + <option value="text" selected="true">ID File (tabular)</option> + </param> + </when> + <when value="neighbor_history"> + <expand macro="db_db_link_macro" name="link_select" label="Link name" /> + <param name="output_format" type="select" label="Output Format"> + <option value="json">History File (json)</option> + <option value="xml" selected="true">History File (xml)</option> + </param> + </when> + <when value="neighbor_score"> + <expand macro="db_db_link_macro" name="link_select" label="Link name" /> + <param name="output_format" type="select" label="Output Format"> + <option value="xml">ID File (xml)</option> + <option value="json">ID File (json)</option> + <option value="text" selected="true">ID File (tabular)</option> + </param> + </when> + <when value="acheck"> + <expand macro="db_link_macro" name="db_select_from_link" label="From NCBI Database" /> + <param name="output_format" type="select" label="Output Format"> + <option value="xml" selected="True">Link Description File (xml)</option> + <option value="json">Link Description File (json)</option> + </param> + </when> + <when value="ncheck"> + <expand macro="db_link_macro" name="db_select_from_link" label="From NCBI Database" /> + <param name="output_format" type="select" label="Output Format"> + <option value="xml" selected="True">Link Description File (xml)</option> + <option value="json">Link Description File (json)</option> + </param> + </when> + <when value="lcheck"> + <expand macro="db_link_macro" name="db_select_from_link" label="From NCBI Database" /> + <param name="output_format" type="select" label="Output Format"> + <option value="xml" selected="True">Link Description File (xml)</option> + <option value="json">Link Description File (json)</option> + </param> + </when> + <when value="llinks"> + <expand macro="db_link_macro" name="db_select_from_link" label="From NCBI Database" /> + <param name="output_format" type="select" label="Output Format"> + <option value="xml" selected="True">Link Description File (xml)</option> + <option value="json">Link Description File (json)</option> + </param> + </when> + <when value="llinkslib"> + <expand macro="db_link_macro" name="db_select_from_link" label="From NCBI Database" /> + <param name="output_format" type="select" label="Output Format"> + <option value="xml" selected="true">Link Description File (xml)</option> + <option value="json">Link Description File (json)</option> + </param> + </when> + <when value="prlinks"> + <expand macro="db_link_macro" name="db_select_from_link" label="From NCBI Database" /> + <param name="output_format" type="select" label="Output Format"> + <option value="xml" selected="true">Link Description File (xml)</option> + <option value="json">Link Description File (json)</option> + </param> + </when> + </conditional> + </xml> + <xml name="db_db_link_macro"> + <conditional name="db_from_link"> + <expand macro="dbselect_linked" name="db_select_from_link" label="From NCBI Database" /> + <when value="annotinfo"> + <conditional name="db_to"> + <param name="db_select_to" type="select" label="To NCBI Database"> + <option value="annotinfo">AnnotInfo (annotinfo)</option> + </param> + <when value="annotinfo"> + <param name="linkname" type="select" label="Link Name"> + <option value="none">All Links</option> + </param> + </when> + </conditional> + </when> + <when value="assembly"> + <conditional name="db_to"> + <param name="db_select_to" type="select" label="To NCBI Database"> + <option value="assembly">Assembly (assembly)</option> + <option value="bioproject">BioProject (bioproject)</option> + <option value="biosample">BioSample (biosample)</option> + <option value="genome">Genome (genome)</option> + <option value="nuccore">Nucleotide (nuccore)</option> + <option value="pubmed">PubMed (pubmed)</option> + <option value="sra">SRA (sra)</option> + <option value="taxonomy">Taxonomy (taxonomy)</option> + </param> + <when value="assembly"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="assembly_assembly_diploid">Linked assembly from diploid (assembly_assembly_diploid)</option> + </param> + </when> + <when value="bioproject"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="assembly_bioproject">BioProject (assembly_bioproject)</option> + </param> + </when> + <when value="biosample"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="assembly_biosample">BioSample (assembly_biosample)</option> + </param> + </when> + <when value="genome"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="assembly_genome">Genome (assembly_genome)</option> + </param> + </when> + <when value="nuccore"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="assembly_nuccore_insdc">Nucleotide INSDC (assembly_nuccore_insdc)</option> + <option value="assembly_nuccore_refseq">Nucleotide RefSeq (assembly_nuccore_refseq)</option> + <option value="assembly_nuccore_wgsmaster">WGS Master (assembly_nuccore_wgsmaster)</option> + </param> + </when> + <when value="pubmed"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="assembly_pubmed">PubMed (assembly_pubmed)</option> + </param> + </when> + <when value="sra"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="assembly_sra">Sra Links (assembly_sra)</option> + </param> + </when> + <when value="taxonomy"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="assembly_taxonomy">Taxonomy (assembly_taxonomy)</option> + </param> + </when> + </conditional> + </when> + <when value="bioproject"> + <conditional name="db_to"> + <param name="db_select_to" type="select" label="To NCBI Database"> + <option value="assembly">Assembly (assembly)</option> + <option value="bioproject">BioProject (bioproject)</option> + <option value="biosample">BioSample (biosample)</option> + <option value="gds">GEO DataSets (gds)</option> + <option value="gene">Gene (gene)</option> + <option value="genome">Genome (genome)</option> + <option value="nuccore">Nucleotide (nuccore)</option> + <option value="pmc">PMC (pmc)</option> + <option value="popset">PopSet (popset)</option> + <option value="protein">Protein (protein)</option> + <option value="pubmed">PubMed (pubmed)</option> + <option value="snp">SNP (snp)</option> + <option value="sra">SRA (sra)</option> + <option value="taxonomy">Taxonomy (taxonomy)</option> + <option value="gap">dbGaP (gap)</option> + <option value="dbvar">dbVar (dbvar)</option> + </param> + <when value="assembly"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="bioproject_assembly_all">Assembly Links (bioproject_assembly_all)</option> + </param> + </when> + <when value="bioproject"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="bioproject_bioproject">BioProject (bioproject_bioproject)</option> + <option value="bioproject_bioproject_u2d">Data projects (bioproject_bioproject_u2d)</option> + <option value="bioproject_bioproject_d2u">Umbrella projects (bioproject_bioproject_d2u)</option> + </param> + </when> + <when value="biosample"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="bioproject_biosample_all">BioSample Links (bioproject_biosample_all)</option> + </param> + </when> + <when value="gds"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="bioproject_gds">GEO DataSet Links (bioproject_gds)</option> + </param> + </when> + <when value="gene"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="bioproject_gene">Related Genes (bioproject_gene)</option> + </param> + </when> + <when value="genome"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="bioproject_genome">Genome Links (bioproject_genome)</option> + </param> + </when> + <when value="nuccore"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="bioproject_nuccore_genomic_dna">Genomic DNA (bioproject_nuccore_genomic_dna)</option> + <option value="bioproject_nuccore_genomic_rna">Genomic RNA (bioproject_nuccore_genomic_rna)</option> + <option value="bioproject_nuccore_map">Map Records (bioproject_nuccore_map)</option> + <option value="bioproject_nuccore">Nucleotide Links (bioproject_nuccore)</option> + <option value="bioproject_nuccore_reference">Reference Genome Sequences Links (bioproject_nuccore_reference)</option> + <option value="bioproject_nuccore_repr">Representative Genome Sequences Links (bioproject_nuccore_repr)</option> + <option value="bioproject_nuccore_tsamaster">TSA master (bioproject_nuccore_tsamaster)</option> + <option value="bioproject_nuccore_transcript">Transcript (bioproject_nuccore_transcript)</option> + <option value="bioproject_nuccore_wgsmaster">WGS master (bioproject_nuccore_wgsmaster)</option> + </param> + </when> + <when value="pmc"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="bioproject_pmc">PMC Links (bioproject_pmc)</option> + </param> + </when> + <when value="popset"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="bioproject_popset">PopSet Links (bioproject_popset)</option> + </param> + </when> + <when value="protein"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="bioproject_protein">Protein Links (bioproject_protein)</option> + </param> + </when> + <when value="pubmed"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="bioproject_pubmed">PubMed Links (bioproject_pubmed)</option> + </param> + </when> + <when value="snp"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="bioproject_snp">SNP Links (bioproject_snp)</option> + </param> + </when> + <when value="sra"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="bioproject_sra_all">SRA Links (bioproject_sra_all)</option> + </param> + </when> + <when value="taxonomy"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="bioproject_taxonomy">Taxonomy Links (bioproject_taxonomy)</option> + </param> + </when> + <when value="gap"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="bioproject_gap">dbGaP Links (bioproject_gap)</option> + </param> + </when> + <when value="dbvar"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="bioproject_dbvar">dbVar (bioproject_dbvar)</option> + </param> + </when> + </conditional> + </when> + <when value="biosample"> + <conditional name="db_to"> + <param name="db_select_to" type="select" label="To NCBI Database"> + <option value="assembly">Assembly (assembly)</option> + <option value="bioproject">BioProject (bioproject)</option> + <option value="biocollections">Biocollections (biocollections)</option> + <option value="gds">GEO DataSets (gds)</option> + <option value="nuccore">Nucleotide (nuccore)</option> + <option value="omim">OMIM (omim)</option> + <option value="pubmed">PubMed (pubmed)</option> + <option value="snp">SNP (snp)</option> + <option value="sra">SRA (sra)</option> + <option value="taxonomy">Taxonomy (taxonomy)</option> + <option value="gap">dbGaP (gap)</option> + <option value="dbvar">dbVar (dbvar)</option> + </param> + <when value="assembly"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="biosample_assembly">Assembly links (biosample_assembly)</option> + </param> + </when> + <when value="bioproject"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="biosample_bioproject">BioProject Links (biosample_bioproject)</option> + </param> + </when> + <when value="biocollections"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="biosample_biocollections">BioCollections (biosample_biocollections)</option> + </param> + </when> + <when value="gds"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="biosample_gds">GEO DataSets Links (biosample_gds)</option> + </param> + </when> + <when value="nuccore"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="biosample_nuccore">Nucleotide Links (biosample_nuccore)</option> + </param> + </when> + <when value="omim"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="biosample_omim">OMIM links (biosample_omim)</option> + </param> + </when> + <when value="pubmed"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="biosample_pubmed">PubMed Links (biosample_pubmed)</option> + </param> + </when> + <when value="snp"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="biosample_snp">SNP Links (biosample_snp)</option> + </param> + </when> + <when value="sra"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="biosample_sra">SRA Links (biosample_sra)</option> + </param> + </when> + <when value="taxonomy"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="biosample_taxonomy">Taxonomy Links (biosample_taxonomy)</option> + </param> + </when> + <when value="gap"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="biosample_gap">dbGaP Links (biosample_gap)</option> + </param> + </when> + <when value="dbvar"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="biosample_dbvar">dbVar Links (biosample_dbvar)</option> + </param> + </when> + </conditional> + </when> + <when value="biosystems"> + <conditional name="db_to"> + <param name="db_select_to" type="select" label="To NCBI Database"> + <option value="biosystems">BioSystems (biosystems)</option> + <option value="cdd">Conserved Domains (cdd)</option> + <option value="geoprofiles">GEO Profiles (geoprofiles)</option> + <option value="gene">Gene (gene)</option> + <option value="homologene">HomoloGene (homologene)</option> + <option value="medgen">MedGen (medgen)</option> + <option value="nuccore">Nucleotide (nuccore)</option> + <option value="omim">OMIM (omim)</option> + <option value="pmc">PMC (pmc)</option> + <option value="protein">Protein (protein)</option> + <option value="proteinclusters">Protein Clusters (proteinclusters)</option> + <option value="pccompound">PubChem Compound (pccompound)</option> + <option value="pcsubstance">PubChem Substance (pcsubstance)</option> + <option value="pubmed">PubMed (pubmed)</option> + <option value="sparcle">Sparcle (sparcle)</option> + <option value="structure">Structure (structure)</option> + <option value="taxonomy">Taxonomy (taxonomy)</option> + <option value="dbvar">dbVar (dbvar)</option> + </param> + <when value="biosystems"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="biosystems_biosystems_conserved">Conserved BioSystems (biosystems_biosystems_conserved)</option> + <option value="biosystems_biosystems_linked">Linked BioSystems (biosystems_biosystems_linked)</option> + <option value="biosystems_biosystems_specific">Organism Specific BioSystems (biosystems_biosystems_specific)</option> + <option value="biosystems_biosystems_similar">Similar BioSystems (biosystems_biosystems_similar)</option> + <option value="biosystems_biosystems_sub">Subset BioSystems (biosystems_biosystems_sub)</option> + <option value="biosystems_biosystems_super">Superset BioSystems (biosystems_biosystems_super)</option> + </param> + </when> + <when value="cdd"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="biosystems_cdd_specific">Conserved Domains (biosystems_cdd_specific)</option> + </param> + </when> + <when value="geoprofiles"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="biosystems_geoprofiles_gene">Gene Expression (biosystems_geoprofiles_gene)</option> + </param> + </when> + <when value="gene"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="biosystems_gene_all">Gene (all) (biosystems_gene_all)</option> + </param> + </when> + <when value="homologene"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="biosystems_homologene">Homologene (biosystems_homologene)</option> + </param> + </when> + <when value="medgen"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="biosystems_medgen_gene_diseases">Medical genetics (biosystems_medgen_gene_diseases)</option> + </param> + </when> + <when value="nuccore"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="biosystems_nuccore">Nucleotides (biosystems_nuccore)</option> + </param> + </when> + <when value="omim"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="biosystems_omim">OMIM (biosystems_omim)</option> + </param> + </when> + <when value="pmc"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="biosystems_pmc_pubmed">Full text in PMC (biosystems_pmc_pubmed)</option> + </param> + </when> + <when value="protein"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="biosystems_protein">Proteins (biosystems_protein)</option> + </param> + </when> + <when value="proteinclusters"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="biosystems_proteinclusters">Protein Clusters (biosystems_proteinclusters)</option> + </param> + </when> + <when value="pccompound"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="biosystems_pccompound">PubChem Compounds (biosystems_pccompound)</option> + </param> + </when> + <when value="pcsubstance"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="biosystems_pcsubstance">PubChem Substances (biosystems_pcsubstance)</option> + </param> + </when> + <when value="pubmed"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="biosystems_pubmed">PubMed (biosystems_pubmed)</option> + </param> + </when> + <when value="sparcle"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="biosystems_sparcle">Functional Class (biosystems_sparcle)</option> + </param> + </when> + <when value="structure"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="biosystems_structure">Structures (biosystems_structure)</option> + </param> + </when> + <when value="taxonomy"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="biosystems_taxonomy">Taxonomy (biosystems_taxonomy)</option> + </param> + </when> + <when value="dbvar"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="biosystems_dbvar_gene">dbVar (biosystems_dbvar_gene)</option> + </param> + </when> + </conditional> + </when> + <when value="biocollections"> + <conditional name="db_to"> + <param name="db_select_to" type="select" label="To NCBI Database"> + <option value="biosample">BioSample (biosample)</option> + <option value="nuccore">Nucleotide (nuccore)</option> + <option value="popset">PopSet (popset)</option> + <option value="protein">Protein (protein)</option> + </param> + <when value="biosample"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="biocollections_biosample">BioSample (biocollections_biosample)</option> + </param> + </when> + <when value="nuccore"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="biocollections_nuccore">Nucleotide (biocollections_nuccore)</option> + </param> + </when> + <when value="popset"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="biocollections_popset">PopSet (biocollections_popset)</option> + </param> + </when> + <when value="protein"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="biocollections_protein">Protein (biocollections_protein)</option> + </param> + </when> + </conditional> + </when> + <when value="blastdbinfo"> + <conditional name="db_to"> + <param name="db_select_to" type="select" label="To NCBI Database"> + <option value="bioproject">BioProject (bioproject)</option> + <option value="pubmed">PubMed (pubmed)</option> + <option value="taxonomy">Taxonomy (taxonomy)</option> + </param> + <when value="bioproject"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="blastdbinfo_bioproject">BioProject Links (blastdbinfo_bioproject)</option> + </param> + </when> + <when value="pubmed"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="blastdbinfo_pubmed">Pubmed Links (blastdbinfo_pubmed)</option> + </param> + </when> + <when value="taxonomy"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="blastdbinfo_taxonomy">Taxonomy Links (blastdbinfo_taxonomy)</option> + </param> + </when> + </conditional> + </when> + <when value="books"> + <conditional name="db_to"> + <param name="db_select_to" type="select" label="To NCBI Database"> + <option value="gene">Gene (gene)</option> + <option value="medgen">MedGen (medgen)</option> + <option value="nlmcatalog">NLM Catalog (nlmcatalog)</option> + <option value="omim">OMIM (omim)</option> + <option value="pmc">PMC (pmc)</option> + <option value="pcassay">PubChem BioAssay (pcassay)</option> + <option value="pcsubstance">PubChem Substance (pcsubstance)</option> + <option value="pubmed">PubMed (pubmed)</option> + <option value="taxonomy">Taxonomy (taxonomy)</option> + </param> + <when value="gene"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="books_gene">Gene Links (books_gene)</option> + </param> + </when> + <when value="medgen"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="books_medgen">MedGen (books_medgen)</option> + </param> + </when> + <when value="nlmcatalog"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="books_nlmcatalog">NLM Catalog Links (books_nlmcatalog)</option> + </param> + </when> + <when value="omim"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="books_omim">OMIM Links (books_omim)</option> + </param> + </when> + <when value="pmc"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="books_pmc_refs">PMC Links (books_pmc_refs)</option> + </param> + </when> + <when value="pcassay"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="books_pcassay_probe">PubChem BioAssay for Chemical Probe (books_pcassay_probe)</option> + </param> + </when> + <when value="pcsubstance"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="books_pcsubstance">PubChem Substance (books_pcsubstance)</option> + </param> + </when> + <when value="pubmed"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="books_pubmed_refs">PubMed Links (books_pubmed_refs)</option> + </param> + </when> + <when value="taxonomy"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="books_taxonomy">Taxonomy Links (books_taxonomy)</option> + </param> + </when> + </conditional> + </when> + <when value="clinvar"> + <conditional name="db_to"> + <param name="db_select_to" type="select" label="To NCBI Database"> + <option value="gtr">GTR (gtr)</option> + <option value="gene">Gene (gene)</option> + <option value="medgen">MedGen (medgen)</option> + <option value="omim">OMIM (omim)</option> + <option value="orgtrack">Orgtrack (orgtrack)</option> + <option value="pmc">PMC (pmc)</option> + <option value="pubmed">PubMed (pubmed)</option> + <option value="snp">SNP (snp)</option> + <option value="sparcle">Sparcle (sparcle)</option> + <option value="dbvar">dbVar (dbvar)</option> + </param> + <when value="gtr"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="clinvar_gtr">GTR (all) (clinvar_gtr)</option> + </param> + </when> + <when value="gene"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="clinvar_gene">Gene (clinvar_gene)</option> + <option value="clinvar_gene_specific">Related genes (specific) (clinvar_gene_specific)</option> + </param> + </when> + <when value="medgen"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="clinvar_medgen">MedGen (clinvar_medgen)</option> + </param> + </when> + <when value="omim"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="clinvar_omim">OMIM (clinvar_omim)</option> + </param> + </when> + <when value="orgtrack"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="clinvar_orgtrack">Orgtrack (all) (clinvar_orgtrack)</option> + </param> + </when> + <when value="pmc"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="clinvar_pmc">PMC (clinvar_pmc)</option> + </param> + </when> + <when value="pubmed"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="clinvar_pubmed_calculated">PubMed (calculated) (clinvar_pubmed_calculated)</option> + <option value="clinvar_pubmed">PubMed (clinvar_pubmed)</option> + </param> + </when> + <when value="snp"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="clinvar_snp">dbSNP (clinvar_snp)</option> + </param> + </when> + <when value="sparcle"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="clinvar_sparcle">Functional Class (clinvar_sparcle)</option> + </param> + </when> + <when value="dbvar"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="clinvar_dbvar">dbVar (clinvar_dbvar)</option> + </param> + </when> + </conditional> + </when> + <when value="cdd"> + <conditional name="db_to"> + <param name="db_select_to" type="select" label="To NCBI Database"> + <option value="biosystems">BioSystems (biosystems)</option> + <option value="cdd">Conserved Domains (cdd)</option> + <option value="gene">Gene (gene)</option> + <option value="homologene">HomoloGene (homologene)</option> + <option value="pmc">PMC (pmc)</option> + <option value="protein">Protein (protein)</option> + <option value="pcassay">PubChem BioAssay (pcassay)</option> + <option value="pubmed">PubMed (pubmed)</option> + <option value="sparcle">Sparcle (sparcle)</option> + <option value="structure">Structure (structure)</option> + <option value="taxonomy">Taxonomy (taxonomy)</option> + </param> + <when value="biosystems"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="cdd_biosystems_specific">BioSystems (cdd_biosystems_specific)</option> + </param> + </when> + <when value="cdd"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="cdd_cdd_superfamily_2">Superfamily Links (cdd_cdd_superfamily_2)</option> + <option value="cdd_cdd_related">Superfamily Member Links (cdd_cdd_related)</option> + </param> + </when> + <when value="gene"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="cdd_gene">Gene Links (cdd_gene)</option> + </param> + </when> + <when value="homologene"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="cdd_homologene">HomoloGene Links (cdd_homologene)</option> + </param> + </when> + <when value="pmc"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="cdd_pmc">PMC Links (cdd_pmc)</option> + </param> + </when> + <when value="protein"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="cdd_protein_summary"> (cdd_protein_summary)</option> + <option value="cdd_protein">Protein Links (cdd_protein)</option> + <option value="cdd_protein_specific_2">Specific Protein Links (cdd_protein_specific_2)</option> + </param> + </when> + <when value="pcassay"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="cdd_pcassay_protein_target">BioAssay via Protein Target (cdd_pcassay_protein_target)</option> + </param> + </when> + <when value="pubmed"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="cdd_pubmed">PubMed Links (cdd_pubmed)</option> + </param> + </when> + <when value="sparcle"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="cdd_sparcle">Functional Class (cdd_sparcle)</option> + </param> + </when> + <when value="structure"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="cdd_structure_family_2">Family Structure Links (cdd_structure_family_2)</option> + <option value="cdd_structure">Structure Links (cdd_structure)</option> + </param> + </when> + <when value="taxonomy"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="cdd_taxonomy">Taxonomy Links (cdd_taxonomy)</option> + </param> + </when> + </conditional> + </when> + <when value="gds"> + <conditional name="db_to"> + <param name="db_select_to" type="select" label="To NCBI Database"> + <option value="bioproject">BioProject (bioproject)</option> + <option value="biosample">BioSample (biosample)</option> + <option value="gds">GEO DataSets (gds)</option> + <option value="geoprofiles">GEO Profiles (geoprofiles)</option> + <option value="pmc">PMC (pmc)</option> + <option value="pubmed">PubMed (pubmed)</option> + <option value="sra">SRA (sra)</option> + <option value="taxonomy">Taxonomy (taxonomy)</option> + <option value="dbvar">dbVar (dbvar)</option> + </param> + <when value="bioproject"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="gds_bioproject">BioProject Links (gds_bioproject)</option> + </param> + </when> + <when value="biosample"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="gds_biosample">BioSample links (gds_biosample)</option> + </param> + </when> + <when value="gds"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="gds_gds">Related DataSets (gds_gds)</option> + <option value="gds_gds_similar">Similar studies (gds_gds_similar)</option> + </param> + </when> + <when value="geoprofiles"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="gds_geoprofiles">GEO Profiles (gds_geoprofiles)</option> + </param> + </when> + <when value="pmc"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="gds_pmc">PMC Links (gds_pmc)</option> + </param> + </when> + <when value="pubmed"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="gds_pubmed">PubMed Links (gds_pubmed)</option> + </param> + </when> + <when value="sra"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="gds_sra">SRA Links (gds_sra)</option> + </param> + </when> + <when value="taxonomy"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="gds_taxonomy">Taxonomy Links (gds_taxonomy)</option> + </param> + </when> + <when value="dbvar"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="gds_dbvar">dbVar Links (gds_dbvar)</option> + </param> + </when> + </conditional> + </when> + <when value="geoprofiles"> + <conditional name="db_to"> + <param name="db_select_to" type="select" label="To NCBI Database"> + <option value="biosystems">BioSystems (biosystems)</option> + <option value="gds">GEO DataSets (gds)</option> + <option value="geoprofiles">GEO Profiles (geoprofiles)</option> + <option value="gene">Gene (gene)</option> + <option value="homologene">HomoloGene (homologene)</option> + <option value="nuccore">Nucleotide (nuccore)</option> + <option value="omim">OMIM (omim)</option> + <option value="pmc">PMC (pmc)</option> + <option value="pubmed">PubMed (pubmed)</option> + <option value="sparcle">Sparcle (sparcle)</option> + <option value="taxonomy">Taxonomy (taxonomy)</option> + </param> + <when value="biosystems"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="geoprofiles_biosystems_gene">Pathways + GO (geoprofiles_biosystems_gene)</option> + </param> + </when> + <when value="gds"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="geoprofiles_gds">Related DataSets (geoprofiles_gds)</option> + </param> + </when> + <when value="geoprofiles"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="geoprofiles_geoprofiles_chr">Chromosome neighbors (geoprofiles_geoprofiles_chr)</option> + <option value="geoprofiles_geoprofiles_homologs">Homologene neighbors (geoprofiles_geoprofiles_homologs)</option> + <option value="geoprofiles_geoprofiles_prof">Profile neighbors (geoprofiles_geoprofiles_prof)</option> + </param> + </when> + <when value="gene"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="geoprofiles_gene">Gene Links (geoprofiles_gene)</option> + </param> + </when> + <when value="homologene"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="geoprofiles_homologene">HomoloGene Links (geoprofiles_homologene)</option> + </param> + </when> + <when value="nuccore"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="geoprofiles_nuccore">Nucleotide Links (geoprofiles_nuccore)</option> + </param> + </when> + <when value="omim"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="geoprofiles_omim">OMIM Links (geoprofiles_omim)</option> + </param> + </when> + <when value="pmc"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="geoprofiles_pmc">PMC Links (geoprofiles_pmc)</option> + </param> + </when> + <when value="pubmed"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="geoprofiles_pubmed">PubMed Links (geoprofiles_pubmed)</option> + </param> + </when> + <when value="sparcle"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="geoprofiles_sparcle">Functional Class (geoprofiles_sparcle)</option> + </param> + </when> + <when value="taxonomy"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="geoprofiles_taxonomy">Taxonomy Links (geoprofiles_taxonomy)</option> + </param> + </when> + </conditional> + </when> + <when value="gtr"> + <conditional name="db_to"> + <param name="db_select_to" type="select" label="To NCBI Database"> + <option value="gene">Gene (gene)</option> + <option value="medgen">MedGen (medgen)</option> + <option value="omim">OMIM (omim)</option> + <option value="orgtrack">Orgtrack (orgtrack)</option> + <option value="sparcle">Sparcle (sparcle)</option> + </param> + <when value="gene"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="gtr_gene">Gene (all) (gtr_gene)</option> + </param> + </when> + <when value="medgen"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="gtr_medgen">MedGen (gtr_medgen)</option> + </param> + </when> + <when value="omim"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="gtr_omim">OMIM (gtr_omim)</option> + </param> + </when> + <when value="orgtrack"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="gtr_orgtrack">Orgtrack (gtr_orgtrack)</option> + </param> + </when> + <when value="sparcle"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="gtr_sparcle">Functional Class (gtr_sparcle)</option> + </param> + </when> + </conditional> + </when> + <when value="gapplus"> + <conditional name="db_to"> + <param name="db_select_to" type="select" label="To NCBI Database"> + <option value="gapplus">GaPPlus (gapplus)</option> + </param> + <when value="gapplus"> + <param name="linkname" type="select" label="Link Name"> + <option value="none">All Links</option> + </param> + </when> + </conditional> + </when> + <when value="gene"> + <conditional name="db_to"> + <param name="db_select_to" type="select" label="To NCBI Database"> + <option value="bioproject">BioProject (bioproject)</option> + <option value="biosystems">BioSystems (biosystems)</option> + <option value="books">Books (books)</option> + <option value="clinvar">ClinVar (clinvar)</option> + <option value="cdd">Conserved Domains (cdd)</option> + <option value="geoprofiles">GEO Profiles (geoprofiles)</option> + <option value="gtr">GTR (gtr)</option> + <option value="gene">Gene (gene)</option> + <option value="genome">Genome (genome)</option> + <option value="homologene">HomoloGene (homologene)</option> + <option value="medgen">MedGen (medgen)</option> + <option value="nuccore">Nucleotide (nuccore)</option> + <option value="nucleotide">Nucleotide (nucleotide)</option> + <option value="omim">OMIM (omim)</option> + <option value="pmc">PMC (pmc)</option> + <option value="protein">Protein (protein)</option> + <option value="proteinclusters">Protein Clusters (proteinclusters)</option> + <option value="pcassay">PubChem BioAssay (pcassay)</option> + <option value="pccompound">PubChem Compound (pccompound)</option> + <option value="pcsubstance">PubChem Substance (pcsubstance)</option> + <option value="pubmed">PubMed (pubmed)</option> + <option value="snp">SNP (snp)</option> + <option value="sparcle">Sparcle (sparcle)</option> + <option value="structure">Structure (structure)</option> + <option value="taxonomy">Taxonomy (taxonomy)</option> + <option value="gap">dbGaP (gap)</option> + <option value="dbvar">dbVar (dbvar)</option> + </param> + <when value="bioproject"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="gene_bioproject">BioProjects (gene_bioproject)</option> + </param> + </when> + <when value="biosystems"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="gene_biosystems">BioSystem Links (gene_biosystems)</option> + </param> + </when> + <when value="books"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="gene_books">Books Links (gene_books)</option> + </param> + </when> + <when value="clinvar"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="gene_clinvar">ClinVar (gene_clinvar)</option> + <option value="gene_clinvar_specific">Related gene-specific medical variations (gene_clinvar_specific)</option> + </param> + </when> + <when value="cdd"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="gene_cdd">Conserved Domain Links (gene_cdd)</option> + </param> + </when> + <when value="geoprofiles"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="gene_geoprofiles">GEO Profile Links (gene_geoprofiles)</option> + </param> + </when> + <when value="gtr"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="gene_gtr">GTR (gene_gtr)</option> + </param> + </when> + <when value="gene"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="gene_gene_neighbors">Gene neighbors (gene_gene_neighbors)</option> + <option value="gene_gene_h3k4me3">Genes with a similar H3K4me3 profile (gene_gene_h3k4me3)</option> + </param> + </when> + <when value="genome"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="gene_genome">Genome Links (gene_genome)</option> + </param> + </when> + <when value="homologene"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="gene_homologene">HomoloGene Links (gene_homologene)</option> + </param> + </when> + <when value="medgen"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="gene_medgen_diseases">MedGen (gene_medgen_diseases)</option> + </param> + </when> + <when value="nuccore"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="gene_nuccore">Nucleotide Links (gene_nuccore)</option> + <option value="gene_nuccore_mgc">Nucleotide NIH cDNA clone links (gene_nuccore_mgc)</option> + <option value="gene_nuccore_refseqrna">RefSeq RNA Links (gene_nuccore_refseqrna)</option> + <option value="gene_nuccore_refseqgene">RefSeqGene Links (gene_nuccore_refseqgene)</option> + </param> + </when> + <when value="nucleotide"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="gene_nucleotide_mgc_url"> (gene_nucleotide_mgc_url)</option> + </param> + </when> + <when value="omim"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="gene_omim">OMIM Links (gene_omim)</option> + </param> + </when> + <when value="pmc"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="gene_pmc_nucleotide">Full text in PMC (nucleotide) (gene_pmc_nucleotide)</option> + <option value="gene_pmc">PMC Links (gene_pmc)</option> + </param> + </when> + <when value="protein"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="gene_protein">Protein Links (gene_protein)</option> + <option value="gene_protein_refseq">RefSeq Protein Links (gene_protein_refseq)</option> + </param> + </when> + <when value="proteinclusters"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="gene_proteinclusters">Protein Cluster Links (gene_proteinclusters)</option> + </param> + </when> + <when value="pcassay"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="gene_pcassay_alltarget_list">BioAssay by Target (List) (gene_pcassay_alltarget_list)</option> + <option value="gene_pcassay_alltarget_summary">BioAssay by Target (Summary) (gene_pcassay_alltarget_summary)</option> + <option value="gene_pcassay_target">BioAssay, by Gene target (gene_pcassay_target)</option> + <option value="gene_pcassay_rnai_active">BioAssays, RNAi Target, Active (gene_pcassay_rnai_active)</option> + <option value="gene_pcassay_rnai">BioAssays, RNAi Target, Tested (gene_pcassay_rnai)</option> + </param> + </when> + <when value="pccompound"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="gene_pccompound">PubChem Compound Links (gene_pccompound)</option> + </param> + </when> + <when value="pcsubstance"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="gene_pcsubstance">PubChem Substance Links (gene_pcsubstance)</option> + </param> + </when> + <when value="pubmed"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="gene_pubmed_rif">PubMed (GeneRIF) Links (gene_pubmed_rif)</option> + <option value="gene_pubmed_citedinomim">PubMed (OMIM) Links (gene_pubmed_citedinomim)</option> + <option value="gene_pubmed_pmc_nucleotide">PubMed (nucleotide/PMC) (gene_pubmed_pmc_nucleotide)</option> + <option value="gene_pubmed">PubMed Links (gene_pubmed)</option> + </param> + </when> + <when value="snp"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="gene_snp_geneview"> (gene_snp_geneview)</option> + <option value="gene_snp">SNP Links (gene_snp)</option> + </param> + </when> + <when value="sparcle"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="gene_sparcle">Functional Class (gene_sparcle)</option> + </param> + </when> + <when value="structure"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="gene_structure">3D structures (gene_structure)</option> + </param> + </when> + <when value="taxonomy"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="gene_taxonomy">Taxonomy Links (gene_taxonomy)</option> + </param> + </when> + <when value="gap"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="gene_gap">GAP Links (gene_gap)</option> + </param> + </when> + <when value="dbvar"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="gene_dbvar">dbVar (gene_dbvar)</option> + </param> + </when> + </conditional> + </when> + <when value="genome"> + <conditional name="db_to"> + <param name="db_select_to" type="select" label="To NCBI Database"> + <option value="assembly">Assembly (assembly)</option> + <option value="bioproject">BioProject (bioproject)</option> + <option value="gene">Gene (gene)</option> + <option value="nuccore">Nucleotide (nuccore)</option> + <option value="protein">Protein (protein)</option> + <option value="proteinclusters">Protein Clusters (proteinclusters)</option> + <option value="pubmed">PubMed (pubmed)</option> + <option value="taxonomy">Taxonomy (taxonomy)</option> + </param> + <when value="assembly"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="genome_assembly">Assembly (genome_assembly)</option> + </param> + </when> + <when value="bioproject"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="genome_bioproject">BioProject Links (genome_bioproject)</option> + </param> + </when> + <when value="gene"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="genome_gene">Gene Links (genome_gene)</option> + </param> + </when> + <when value="nuccore"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="genome_nuccore">Components (genome_nuccore)</option> + <option value="genome_nuccore_samespecies">Other genomes for species (genome_nuccore_samespecies)</option> + </param> + </when> + <when value="protein"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="genome_protein">Protein Links (genome_protein)</option> + </param> + </when> + <when value="proteinclusters"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="genome_proteinclusters">Protein Cluster Links (genome_proteinclusters)</option> + </param> + </when> + <when value="pubmed"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="genome_pubmed">PubMed Links (genome_pubmed)</option> + </param> + </when> + <when value="taxonomy"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="genome_taxonomy">Taxonomy Links (genome_taxonomy)</option> + </param> + </when> + </conditional> + </when> + <when value="homologene"> + <conditional name="db_to"> + <param name="db_select_to" type="select" label="To NCBI Database"> + <option value="biosystems">BioSystems (biosystems)</option> + <option value="cdd">Conserved Domains (cdd)</option> + <option value="geoprofiles">GEO Profiles (geoprofiles)</option> + <option value="gene">Gene (gene)</option> + <option value="homologene">HomoloGene (homologene)</option> + <option value="nuccore">Nucleotide (nuccore)</option> + <option value="omim">OMIM (omim)</option> + <option value="pmc">PMC (pmc)</option> + <option value="protein">Protein (protein)</option> + <option value="pubmed">PubMed (pubmed)</option> + <option value="sparcle">Sparcle (sparcle)</option> + <option value="taxonomy">Taxonomy (taxonomy)</option> + </param> + <when value="biosystems"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="homologene_biosystems">BioSystems (homologene_biosystems)</option> + </param> + </when> + <when value="cdd"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="homologene_cdd">Conserved Domain Links (homologene_cdd)</option> + </param> + </when> + <when value="geoprofiles"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="homologene_geoprofiles">GEO Profile Links (homologene_geoprofiles)</option> + </param> + </when> + <when value="gene"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="homologene_gene">Gene Links (homologene_gene)</option> + </param> + </when> + <when value="homologene"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="homologene_homologene">Related HomoloGene Links (homologene_homologene)</option> + </param> + </when> + <when value="nuccore"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="homologene_nuccore">Nucleotide Links (homologene_nuccore)</option> + </param> + </when> + <when value="omim"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="homologene_omim">OMIM Links (homologene_omim)</option> + </param> + </when> + <when value="pmc"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="homologene_pmc">PMC Links (homologene_pmc)</option> + </param> + </when> + <when value="protein"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="homologene_protein">Protein Links (homologene_protein)</option> + </param> + </when> + <when value="pubmed"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="homologene_pubmed">PubMed Links (homologene_pubmed)</option> + </param> + </when> + <when value="sparcle"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="homologene_sparcle">Functional Class (homologene_sparcle)</option> + </param> + </when> + <when value="taxonomy"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="homologene_taxonomy">Taxonomy Links (homologene_taxonomy)</option> + </param> + </when> + </conditional> + </when> + <when value="ipg"> + <conditional name="db_to"> + <param name="db_select_to" type="select" label="To NCBI Database"> + <option value="bioproject">BioProject (bioproject)</option> + <option value="taxonomy">Taxonomy (taxonomy)</option> + </param> + <when value="bioproject"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="ipg_bioproject">BioProject Links (ipg_bioproject)</option> + </param> + </when> + <when value="taxonomy"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="ipg_taxonomy">Taxonomy Links (ipg_taxonomy)</option> + </param> + </when> + </conditional> + </when> + <when value="mesh"> + <conditional name="db_to"> + <param name="db_select_to" type="select" label="To NCBI Database"> + <option value="medgen">MedGen (medgen)</option> + <option value="pccompound">PubChem Compound (pccompound)</option> + <option value="taxonomy">Taxonomy (taxonomy)</option> + <option value="gap">dbGaP (gap)</option> + </param> + <when value="medgen"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="mesh_medgen">MedGen (mesh_medgen)</option> + </param> + </when> + <when value="pccompound"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="mesh_pccompound">PubChem Compound Links (mesh_pccompound)</option> + </param> + </when> + <when value="taxonomy"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="mesh_taxonomy">Taxonomy Links (mesh_taxonomy)</option> + </param> + </when> + <when value="gap"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="mesh_gap">dbGaP Links (mesh_gap)</option> + </param> + </when> + </conditional> + </when> + <when value="medgen"> + <conditional name="db_to"> + <param name="db_select_to" type="select" label="To NCBI Database"> + <option value="biosystems">BioSystems (biosystems)</option> + <option value="books">Books (books)</option> + <option value="clinvar">ClinVar (clinvar)</option> + <option value="gtr">GTR (gtr)</option> + <option value="gene">Gene (gene)</option> + <option value="mesh">MeSH (mesh)</option> + <option value="omim">OMIM (omim)</option> + <option value="pmc">PMC (pmc)</option> + <option value="pubmed">PubMed (pubmed)</option> + <option value="sparcle">Sparcle (sparcle)</option> + <option value="gap">dbGaP (gap)</option> + </param> + <when value="biosystems"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="medgen_biosystems_gene_diseases">Pathways + GO (medgen_biosystems_gene_diseases)</option> + </param> + </when> + <when value="books"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="medgen_books">NCBI Bookshelf (medgen_books)</option> + </param> + </when> + <when value="clinvar"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="medgen_clinvar">ClinVar (medgen_clinvar)</option> + </param> + </when> + <when value="gtr"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="medgen_gtr">GTR (medgen_gtr)</option> + <option value="medgen_gtr_tests_clinical">GTR(Clinical) (medgen_gtr_tests_clinical)</option> + <option value="medgen_gtr_tests_research">GTR(Research) (medgen_gtr_tests_research)</option> + </param> + </when> + <when value="gene"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="medgen_gene_diseases">Gene (medgen_gene_diseases)</option> + </param> + </when> + <when value="mesh"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="medgen_mesh">MeSH (medgen_mesh)</option> + </param> + </when> + <when value="omim"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="medgen_omim">OMIM (medgen_omim)</option> + <option value="medgen_omim_gene">OMIM(Genes) (medgen_omim_gene)</option> + </param> + </when> + <when value="pmc"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="medgen_pmc">PMC Articles (medgen_pmc)</option> + </param> + </when> + <when value="pubmed"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="medgen_pubmed_bookshelf_cited">PubMed (Bookshelf cited) (medgen_pubmed_bookshelf_cited)</option> + <option value="medgen_pubmed_genereviews">PubMed (GeneReviews) (medgen_pubmed_genereviews)</option> + <option value="medgen_pubmed_omim">PubMed (OMIM) (medgen_pubmed_omim)</option> + <option value="medgen_pubmed">PubMed (medgen_pubmed)</option> + </param> + </when> + <when value="sparcle"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="medgen_sparcle_diseases">Functional Class (medgen_sparcle_diseases)</option> + </param> + </when> + <when value="gap"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="medgen_gap">dbGaP (medgen_gap)</option> + </param> + </when> + </conditional> + </when> + <when value="ncbisearch"> + <conditional name="db_to"> + <param name="db_select_to" type="select" label="To NCBI Database"> + <option value="ncbisearch">NCBI Web Site (ncbisearch)</option> + </param> + <when value="ncbisearch"> + <param name="linkname" type="select" label="Link Name"> + <option value="none">All Links</option> + </param> + </when> + </conditional> + </when> + <when value="nlmcatalog"> + <conditional name="db_to"> + <param name="db_select_to" type="select" label="To NCBI Database"> + <option value="books">Books (books)</option> + <option value="pubmed">PubMed (pubmed)</option> + </param> + <when value="books"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="nlmcatalog_books">Book Links (nlmcatalog_books)</option> + </param> + </when> + <when value="pubmed"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="nlmcatalog_pubmed">PubMed Links (nlmcatalog_pubmed)</option> + </param> + </when> + </conditional> + </when> + <when value="nuccore"> + <conditional name="db_to"> + <param name="db_select_to" type="select" label="To NCBI Database"> + <option value="assembly">Assembly (assembly)</option> + <option value="bioproject">BioProject (bioproject)</option> + <option value="biosample">BioSample (biosample)</option> + <option value="biosystems">BioSystems (biosystems)</option> + <option value="biocollections">Biocollections (biocollections)</option> + <option value="geoprofiles">GEO Profiles (geoprofiles)</option> + <option value="gene">Gene (gene)</option> + <option value="genome">Genome (genome)</option> + <option value="homologene">HomoloGene (homologene)</option> + <option value="nuccore">Nucleotide (nuccore)</option> + <option value="omim">OMIM (omim)</option> + <option value="pmc">PMC (pmc)</option> + <option value="popset">PopSet (popset)</option> + <option value="protein">Protein (protein)</option> + <option value="proteinclusters">Protein Clusters (proteinclusters)</option> + <option value="pcassay">PubChem BioAssay (pcassay)</option> + <option value="pccompound">PubChem Compound (pccompound)</option> + <option value="pcsubstance">PubChem Substance (pcsubstance)</option> + <option value="pubmed">PubMed (pubmed)</option> + <option value="snp">SNP (snp)</option> + <option value="sra">SRA (sra)</option> + <option value="sparcle">Sparcle (sparcle)</option> + <option value="structure">Structure (structure)</option> + <option value="taxonomy">Taxonomy (taxonomy)</option> + <option value="dbvar">dbVar (dbvar)</option> + </param> + <when value="assembly"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="nuccore_assembly">Assembly (nuccore_assembly)</option> + <option value="nuccore_assembly_wgscontig">Assembly (nuccore_assembly_wgscontig)</option> + </param> + </when> + <when value="bioproject"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="nuccore_bioproject">BioProject Links (nuccore_bioproject)</option> + <option value="nuccore_bioproject_reference">Reference Genome BioProject Links (nuccore_bioproject_reference)</option> + <option value="nuccore_bioproject_repr">Representative Genome BioProject Links (nuccore_bioproject_repr)</option> + </param> + </when> + <when value="biosample"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="nuccore_biosample">BioSample links (nuccore_biosample)</option> + </param> + </when> + <when value="biosystems"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="nuccore_biosystems">BioSystem Links (nuccore_biosystems)</option> + </param> + </when> + <when value="biocollections"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="nuccore_biocollections">BioCollections (nuccore_biocollections)</option> + </param> + </when> + <when value="geoprofiles"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="nuccore_geoprofiles">GEO Profiles Links (nuccore_geoprofiles)</option> + </param> + </when> + <when value="gene"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="nuccore_gene">Gene Links (nuccore_gene)</option> + </param> + </when> + <when value="genome"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="nuccore_genome">Genome (nuccore_genome)</option> + <option value="nuccore_genome_samespecies">RefSeq genome for species (nuccore_genome_samespecies)</option> + </param> + </when> + <when value="homologene"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="nuccore_homologene">HomoloGene Links (nuccore_homologene)</option> + </param> + </when> + <when value="nuccore"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="nuccore_nuccore_mgc_refseq"> (nuccore_nuccore_mgc_refseq)</option> + <option value="nuccore_mrna_nuccore">Annotated Genomic (nuccore_mrna_nuccore)</option> + <option value="nuccore_comp_nuccore">Component Of (nuccore_comp_nuccore)</option> + <option value="nuccore_nuccore_comp">Component(Core) Links (nuccore_nuccore_comp)</option> + <option value="nuccore_nuccore_related">Genomic Neighbours (nuccore_nuccore_related)</option> + <option value="nuccore_nuccore_rsgb">Identical GenBank (nuccore_nuccore_rsgb)</option> + <option value="nuccore_nuccore_gbrs">Identical RefSeq (nuccore_nuccore_gbrs)</option> + <option value="nuccore_nuccore_small_genome">Link to all segments from this genome (nuccore_nuccore_small_genome)</option> + <option value="nuccore_nuccore_samespecies_rsgb">Other nucleotides for species (nuccore_nuccore_samespecies_rsgb)</option> + <option value="nuccore_nuccore_mrna">RNA (nuccore_nuccore_mrna)</option> + <option value="nuccore_nuccore_samespecies_gbrs">RefSeq nucleotide for species (nuccore_nuccore_samespecies_gbrs)</option> + </param> + </when> + <when value="omim"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="nuccore_omim">OMIM Links (nuccore_omim)</option> + </param> + </when> + <when value="pmc"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="nuccore_pmc">PMC Links (nuccore_pmc)</option> + </param> + </when> + <when value="popset"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="nuccore_popset">PopSet Links (nuccore_popset)</option> + </param> + </when> + <when value="protein"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="nuccore_protein_mgc_url"> (nuccore_protein_mgc_url)</option> + <option value="nuccore_protein_wgs"> (nuccore_protein_wgs)</option> + <option value="nuccore_protein_small_genome">Link to all proteins from this genome (nuccore_protein_small_genome)</option> + <option value="nuccore_protein_mat_peptide">Mature Peptides (nuccore_protein_mat_peptide)</option> + <option value="nuccore_protein">Protein Links (nuccore_protein)</option> + <option value="nuccore_protein_tsa_vdb">Protein from TSA (nuccore_protein_tsa_vdb)</option> + <option value="nuccore_protein_wgs_vdb">Protein from WGS (nuccore_protein_wgs_vdb)</option> + <option value="nuccore_protein_tsa">Proteins in this TSA project (nuccore_protein_tsa)</option> + </param> + </when> + <when value="proteinclusters"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="nuccore_proteinclusters">Protein Cluster Links (nuccore_proteinclusters)</option> + </param> + </when> + <when value="pcassay"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="nuccore_pcassay">BioAssay Links (nuccore_pcassay)</option> + <option value="nuccore_pcassay_rna_target">BioAssay by RNA Target (nuccore_pcassay_rna_target)</option> + </param> + </when> + <when value="pccompound"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="nuccore_pccompound">PubChem Compound Links (nuccore_pccompound)</option> + </param> + </when> + <when value="pcsubstance"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="nuccore_pcsubstance">PubChem Substance Links (nuccore_pcsubstance)</option> + </param> + </when> + <when value="pubmed"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="nuccore_pubmed_refseq">PubMed (RefSeq) Links (nuccore_pubmed_refseq)</option> + <option value="nuccore_pubmed_weighted">PubMed (Weighted) Links (nuccore_pubmed_weighted)</option> + <option value="nuccore_pubmed">PubMed Links (nuccore_pubmed)</option> + </param> + </when> + <when value="snp"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="nuccore_snp">SNP Links (nuccore_snp)</option> + </param> + </when> + <when value="sra"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="nuccore_sra">SRA Links (nuccore_sra)</option> + <option value="nuccore_sra_wgs">SRA WGS (nuccore_sra_wgs)</option> + </param> + </when> + <when value="sparcle"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="nuccore_sparcle_mrna">Functional Class (nuccore_sparcle_mrna)</option> + </param> + </when> + <when value="structure"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="nuccore_structure">Structure Links (nuccore_structure)</option> + </param> + </when> + <when value="taxonomy"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="nuccore_taxonomy">Taxonomy Links (nuccore_taxonomy)</option> + </param> + </when> + <when value="dbvar"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="nuccore_dbvar">dbVar (nuccore_dbvar)</option> + </param> + </when> + </conditional> + </when> + <when value="nucleotide"> + <conditional name="db_to"> + <param name="db_select_to" type="select" label="To NCBI Database"> + <option value="genome">Genome (genome)</option> + </param> + <when value="genome"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="nucleotide_genome">Assembly to Genome (nucleotide_genome)</option> + </param> + </when> + </conditional> + </when> + <when value="omim"> + <conditional name="db_to"> + <param name="db_select_to" type="select" label="To NCBI Database"> + <option value="biosample">BioSample (biosample)</option> + <option value="biosystems">BioSystems (biosystems)</option> + <option value="books">Books (books)</option> + <option value="clinvar">ClinVar (clinvar)</option> + <option value="geoprofiles">GEO Profiles (geoprofiles)</option> + <option value="gtr">GTR (gtr)</option> + <option value="gene">Gene (gene)</option> + <option value="homologene">HomoloGene (homologene)</option> + <option value="medgen">MedGen (medgen)</option> + <option value="nuccore">Nucleotide (nuccore)</option> + <option value="omim">OMIM (omim)</option> + <option value="pmc">PMC (pmc)</option> + <option value="protein">Protein (protein)</option> + <option value="pcassay">PubChem BioAssay (pcassay)</option> + <option value="pccompound">PubChem Compound (pccompound)</option> + <option value="pcsubstance">PubChem Substance (pcsubstance)</option> + <option value="pubmed">PubMed (pubmed)</option> + <option value="sra">SRA (sra)</option> + <option value="sparcle">Sparcle (sparcle)</option> + <option value="structure">Structure (structure)</option> + <option value="dbvar">dbVar (dbvar)</option> + </param> + <when value="biosample"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="omim_biosample">OMIM links (omim_biosample)</option> + </param> + </when> + <when value="biosystems"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="omim_biosystems">BioSystem Links (omim_biosystems)</option> + </param> + </when> + <when value="books"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="omim_books">Book Links (omim_books)</option> + </param> + </when> + <when value="clinvar"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="omim_clinvar">ClinVar (omim_clinvar)</option> + </param> + </when> + <when value="geoprofiles"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="omim_geoprofiles">GEO Profile Links (omim_geoprofiles)</option> + </param> + </when> + <when value="gtr"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="omim_gtr">GTR (omim_gtr)</option> + </param> + </when> + <when value="gene"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="omim_gene">Gene Links (omim_gene)</option> + </param> + </when> + <when value="homologene"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="omim_homologene">HomoloGene Links (omim_homologene)</option> + </param> + </when> + <when value="medgen"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="omim_medgen">MedGen (omim_medgen)</option> + <option value="omim_medgen_gene">MedGen (omim_medgen_gene)</option> + </param> + </when> + <when value="nuccore"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="omim_nuccore">Nucleotide Links (omim_nuccore)</option> + </param> + </when> + <when value="omim"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="omim_omim">Related Entries (omim_omim)</option> + </param> + </when> + <when value="pmc"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="omim_pmc">PMC Links (omim_pmc)</option> + </param> + </when> + <when value="protein"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="omim_protein">Protein Links (omim_protein)</option> + </param> + </when> + <when value="pcassay"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="omim_pcassay">PubChem BioAssay Links (omim_pcassay)</option> + </param> + </when> + <when value="pccompound"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="omim_pccompound">PubChem Compound Links (omim_pccompound)</option> + </param> + </when> + <when value="pcsubstance"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="omim_pcsubstance">PubChem Substance Links (omim_pcsubstance)</option> + </param> + </when> + <when value="pubmed"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="omim_pubmed_calculated">PubMed (calculated) Links (omim_pubmed_calculated)</option> + <option value="omim_pubmed_cited">PubMed (cited) Links (omim_pubmed_cited)</option> + </param> + </when> + <when value="sra"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="omim_sra">Omim links (omim_sra)</option> + </param> + </when> + <when value="sparcle"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="omim_sparcle">Functional Class (omim_sparcle)</option> + </param> + </when> + <when value="structure"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="omim_structure">Structure Links (omim_structure)</option> + </param> + </when> + <when value="dbvar"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="omim_dbvar">dbVar (omim_dbvar)</option> + </param> + </when> + </conditional> + </when> + <when value="orgtrack"> + <conditional name="db_to"> + <param name="db_select_to" type="select" label="To NCBI Database"> + <option value="gtr">GTR (gtr)</option> + <option value="gene">Gene (gene)</option> + <option value="medgen">MedGen (medgen)</option> + </param> + <when value="gtr"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="orgtrack_gtr">GTR (orgtrack_gtr)</option> + </param> + </when> + <when value="gene"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="orgtrack_gene">GTR Lab to Genes (orgtrack_gene)</option> + </param> + </when> + <when value="medgen"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="orgtrack_medgen">MedGen (orgtrack_medgen)</option> + </param> + </when> + </conditional> + </when> + <when value="pmc"> + <conditional name="db_to"> + <param name="db_select_to" type="select" label="To NCBI Database"> + <option value="bioproject">BioProject (bioproject)</option> + <option value="biosystems">BioSystems (biosystems)</option> + <option value="books">Books (books)</option> + <option value="clinvar">ClinVar (clinvar)</option> + <option value="cdd">Conserved Domains (cdd)</option> + <option value="gds">GEO DataSets (gds)</option> + <option value="geoprofiles">GEO Profiles (geoprofiles)</option> + <option value="gene">Gene (gene)</option> + <option value="homologene">HomoloGene (homologene)</option> + <option value="medgen">MedGen (medgen)</option> + <option value="nuccore">Nucleotide (nuccore)</option> + <option value="omim">OMIM (omim)</option> + <option value="popset">PopSet (popset)</option> + <option value="protein">Protein (protein)</option> + <option value="pcassay">PubChem BioAssay (pcassay)</option> + <option value="pccompound">PubChem Compound (pccompound)</option> + <option value="pcsubstance">PubChem Substance (pcsubstance)</option> + <option value="pubmed">PubMed (pubmed)</option> + <option value="snp">SNP (snp)</option> + <option value="sra">SRA (sra)</option> + <option value="structure">Structure (structure)</option> + <option value="taxonomy">Taxonomy (taxonomy)</option> + <option value="gap">dbGaP (gap)</option> + </param> + <when value="bioproject"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="pmc_bioproject">BioProject Links (pmc_bioproject)</option> + </param> + </when> + <when value="biosystems"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="pmc_biosystems_pubmed">Pathways + GO (pmc_biosystems_pubmed)</option> + </param> + </when> + <when value="books"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="pmc_books_refs">Cited in Books (pmc_books_refs)</option> + </param> + </when> + <when value="clinvar"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="pmc_clinvar">ClinVar (pmc_clinvar)</option> + </param> + </when> + <when value="cdd"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="pmc_cdd">Conserved Domain Links (pmc_cdd)</option> + </param> + </when> + <when value="gds"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="pmc_gds">GEO DataSet Links (pmc_gds)</option> + </param> + </when> + <when value="geoprofiles"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="pmc_geoprofiles">GEO Profile Links (pmc_geoprofiles)</option> + </param> + </when> + <when value="gene"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="pmc_gene_nucleotide">Gene (nucleotide) (pmc_gene_nucleotide)</option> + <option value="pmc_gene">Gene Links (pmc_gene)</option> + </param> + </when> + <when value="homologene"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="pmc_homologene">HomoloGene Links (pmc_homologene)</option> + </param> + </when> + <when value="medgen"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="pmc_medgen">MedGen (pmc_medgen)</option> + </param> + </when> + <when value="nuccore"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="pmc_nuccore">Nucleotide Links (pmc_nuccore)</option> + </param> + </when> + <when value="omim"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="pmc_omim">OMIM Links (pmc_omim)</option> + </param> + </when> + <when value="popset"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="pmc_popset">PopSet Links (pmc_popset)</option> + </param> + </when> + <when value="protein"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="pmc_protein">Protein Links (pmc_protein)</option> + </param> + </when> + <when value="pcassay"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="pmc_pcassay">BioAssay Links (pmc_pcassay)</option> + </param> + </when> + <when value="pccompound"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="pmc_pccompound">Compound Links (pmc_pccompound)</option> + </param> + </when> + <when value="pcsubstance"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="pmc_pcsubstance">Substance Links (pmc_pcsubstance)</option> + </param> + </when> + <when value="pubmed"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="pmc_pubmed_embargo"> (pmc_pubmed_embargo)</option> + <option value="pmc_refs_pubmed">Cited Articles (pmc_refs_pubmed)</option> + <option value="pmc_pubmed">PubMed Links (pmc_pubmed)</option> + </param> + </when> + <when value="snp"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="pmc_snp">SNP Links (pmc_snp)</option> + </param> + </when> + <when value="sra"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="pmc_sra">SRA (pmc_sra)</option> + </param> + </when> + <when value="structure"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="pmc_structure">Structure Links (pmc_structure)</option> + </param> + </when> + <when value="taxonomy"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="pmc_taxonomy">Taxonomy Links (pmc_taxonomy)</option> + </param> + </when> + <when value="gap"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="pmc_gap">dbGaP Links (pmc_gap)</option> + </param> + </when> + </conditional> + </when> + <when value="popset"> + <conditional name="db_to"> + <param name="db_select_to" type="select" label="To NCBI Database"> + <option value="bioproject">BioProject (bioproject)</option> + <option value="biocollections">Biocollections (biocollections)</option> + <option value="nuccore">Nucleotide (nuccore)</option> + <option value="pmc">PMC (pmc)</option> + <option value="popset">PopSet (popset)</option> + <option value="protein">Protein (protein)</option> + <option value="pubmed">PubMed (pubmed)</option> + <option value="taxonomy">Taxonomy (taxonomy)</option> + </param> + <when value="bioproject"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="popset_bioproject">BioProject Links (popset_bioproject)</option> + </param> + </when> + <when value="biocollections"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="popset_biocollections">BioCollections (popset_biocollections)</option> + </param> + </when> + <when value="nuccore"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="popset_nuccore">Nucleotide Links (popset_nuccore)</option> + </param> + </when> + <when value="pmc"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="popset_pmc"> (popset_pmc)</option> + </param> + </when> + <when value="popset"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="popset_popset">PopSet (popset_popset)</option> + </param> + </when> + <when value="protein"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="popset_protein">Protein Links (popset_protein)</option> + </param> + </when> + <when value="pubmed"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="popset_pubmed">PubMed Links (popset_pubmed)</option> + </param> + </when> + <when value="taxonomy"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="popset_taxonomy">Taxonomy Links (popset_taxonomy)</option> + </param> + </when> + </conditional> + </when> + <when value="protein"> + <conditional name="db_to"> + <param name="db_select_to" type="select" label="To NCBI Database"> + <option value="bioproject">BioProject (bioproject)</option> + <option value="biosystems">BioSystems (biosystems)</option> + <option value="biocollections">Biocollections (biocollections)</option> + <option value="cdd">Conserved Domains (cdd)</option> + <option value="gene">Gene (gene)</option> + <option value="genome">Genome (genome)</option> + <option value="homologene">HomoloGene (homologene)</option> + <option value="nuccore">Nucleotide (nuccore)</option> + <option value="nucleotide">Nucleotide (nucleotide)</option> + <option value="omim">OMIM (omim)</option> + <option value="pmc">PMC (pmc)</option> + <option value="popset">PopSet (popset)</option> + <option value="protein">Protein (protein)</option> + <option value="proteinclusters">Protein Clusters (proteinclusters)</option> + <option value="pcassay">PubChem BioAssay (pcassay)</option> + <option value="pccompound">PubChem Compound (pccompound)</option> + <option value="pcsubstance">PubChem Substance (pcsubstance)</option> + <option value="pubmed">PubMed (pubmed)</option> + <option value="snp">SNP (snp)</option> + <option value="structure">Structure (structure)</option> + <option value="taxonomy">Taxonomy (taxonomy)</option> + </param> + <when value="bioproject"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="protein_bioproject">BioProject Links (protein_bioproject)</option> + </param> + </when> + <when value="biosystems"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="protein_biosystems">BioSystem Links (protein_biosystems)</option> + </param> + </when> + <when value="biocollections"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="protein_biocollections">BioCollections (protein_biocollections)</option> + </param> + </when> + <when value="cdd"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="protein_cdd_summary"> (protein_cdd_summary)</option> + <option value="protein_cdd_concise_2">Concise Conserved Domain Links (protein_cdd_concise_2)</option> + <option value="protein_cdd">Conserved Domain Links (protein_cdd)</option> + </param> + </when> + <when value="gene"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="protein_gene">Gene Links (protein_gene)</option> + </param> + </when> + <when value="genome"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="protein_genome">Genome Links (protein_genome)</option> + </param> + </when> + <when value="homologene"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="protein_homologene">HomoloGene Links (protein_homologene)</option> + </param> + </when> + <when value="nuccore"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="protein_nuccore_wgs"> (protein_nuccore_wgs)</option> + <option value="protein_nuccore_mrna">Encoding mRNA (protein_nuccore_mrna)</option> + <option value="protein_nuccore_small_genome">Link to all nucleotide sequences from this genome (protein_nuccore_small_genome)</option> + <option value="protein_nuccore_wp">Link to genomic records (protein_nuccore_wp)</option> + <option value="nuccore_protein_wp">Links to autonomous proteins (nuccore_protein_wp)</option> + <option value="protein_nuccore_mat_peptide">Mature Peptides (protein_nuccore_mat_peptide)</option> + <option value="protein_nuccore">Nucleotide Links (protein_nuccore)</option> + <option value="protein_nuccore_mgc">Nucleotide NIH cDNA clone links (protein_nuccore_mgc)</option> + <option value="protein_nuccore_tsa">TSA master records (protein_nuccore_tsa)</option> + </param> + </when> + <when value="nucleotide"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="protein_nucleotide_mgc_url"> (protein_nucleotide_mgc_url)</option> + </param> + </when> + <when value="omim"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="protein_omim">OMIM Links (protein_omim)</option> + </param> + </when> + <when value="pmc"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="protein_pmc">PMC Links (protein_pmc)</option> + </param> + </when> + <when value="popset"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="protein_popset">PopSet Links (protein_popset)</option> + </param> + </when> + <when value="protein"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="protein_protein_cdart_summary"> (protein_protein_cdart_summary)</option> + <option value="protein_protein_small_genome">Link to all proteins from this genome (protein_protein_small_genome)</option> + <option value="protein_protein_wp2ref">Link to referencing proteins (protein_protein_wp2ref)</option> + <option value="protein_protein_ref2wp">Links from references to autonomous proteins (protein_protein_ref2wp)</option> + <option value="protein_protein_uniprot2refseq">Protein (RefSeq) (protein_protein_uniprot2refseq)</option> + <option value="protein_protein_refseq2uniprot">Protein (UniProtKB) (protein_protein_refseq2uniprot)</option> + </param> + </when> + <when value="proteinclusters"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="protein_proteinclusters">Protein Cluster Links (protein_proteinclusters)</option> + </param> + </when> + <when value="pcassay"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="protein_pcassay_target_pig">BioAssay by Target (Identical Proteins, List) (protein_pcassay_target_pig)</option> + <option value="protein_pcassay_target">BioAssay by Target (List) (protein_pcassay_target)</option> + <option value="protein_pcassay_target_pig_summary">pcassay (protein_pcassay_target_pig_summary)</option> + <option value="protein_pcassay_target_summary">pcassay (protein_pcassay_target_summary)</option> + </param> + </when> + <when value="pccompound"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="protein_pccompound">PubChem Compound Links (protein_pccompound)</option> + </param> + </when> + <when value="pcsubstance"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="protein_pcsubstance">PubChem Substance Links (protein_pcsubstance)</option> + </param> + </when> + <when value="pubmed"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="protein_pubmed_refseq">PubMed (RefSeq) Links (protein_pubmed_refseq)</option> + <option value="protein_pubmed_weighted">PubMed (Weighted) Links (protein_pubmed_weighted)</option> + <option value="protein_pubmed">PubMed Links (protein_pubmed)</option> + </param> + </when> + <when value="snp"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="protein_snp_geneview"> (protein_snp_geneview)</option> + <option value="protein_snp">SNP Links (protein_snp)</option> + </param> + </when> + <when value="structure"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="protein_structure_related"> (protein_structure_related)</option> + <option value="protein_structure">Identical Structures (protein_structure)</option> + <option value="protein_structure_related_list">Related Structures (List) (protein_structure_related_list)</option> + <option value="protein_structure_direct">Structures (protein_structure_direct)</option> + </param> + </when> + <when value="taxonomy"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="protein_taxonomy_wp2species">Links from autonomous proteins to species level organisms (protein_taxonomy_wp2species)</option> + <option value="protein_taxonomy">Taxonomy Links (protein_taxonomy)</option> + </param> + </when> + </conditional> + </when> + <when value="proteinclusters"> + <conditional name="db_to"> + <param name="db_select_to" type="select" label="To NCBI Database"> + <option value="biosystems">BioSystems (biosystems)</option> + <option value="gene">Gene (gene)</option> + <option value="genome">Genome (genome)</option> + <option value="nuccore">Nucleotide (nuccore)</option> + <option value="protein">Protein (protein)</option> + <option value="pubmed">PubMed (pubmed)</option> + <option value="sparcle">Sparcle (sparcle)</option> + <option value="taxonomy">Taxonomy (taxonomy)</option> + </param> + <when value="biosystems"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="proteinclusters_biosystems">BioSystems (proteinclusters_biosystems)</option> + </param> + </when> + <when value="gene"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="proteinclusters_gene">Gene Links (proteinclusters_gene)</option> + </param> + </when> + <when value="genome"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="proteinclusters_genome">Genome Links (proteinclusters_genome)</option> + </param> + </when> + <when value="nuccore"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="proteinclusters_nuccore">Nucleotide Links (proteinclusters_nuccore)</option> + </param> + </when> + <when value="protein"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="proteinclusters_protein">Protein Links (proteinclusters_protein)</option> + </param> + </when> + <when value="pubmed"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="proteinclusters_pubmed_homology">PubMed (By Homology) Links (proteinclusters_pubmed_homology)</option> + <option value="proteinclusters_pubmed_cdd">PubMed (CDD) Links (proteinclusters_pubmed_cdd)</option> + <option value="proteinclusters_pubmed_curated">PubMed (Curated) Links (proteinclusters_pubmed_curated)</option> + <option value="proteinclusters_pubmed_generif">PubMed (GeneRIF) Links (proteinclusters_pubmed_generif)</option> + <option value="proteinclusters_pubmed_refseq">PubMed (RefSeq) Links (proteinclusters_pubmed_refseq)</option> + <option value="proteinclusters_pubmed_structure">PubMed (Structure) Links (proteinclusters_pubmed_structure)</option> + <option value="proteinclusters_pubmed_swissprot">PubMed (SwissProt) Links (proteinclusters_pubmed_swissprot)</option> + <option value="proteinclusters_pubmed">PubMed Links (proteinclusters_pubmed)</option> + </param> + </when> + <when value="sparcle"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="proteinclusters_sparcle">Functional Class (proteinclusters_sparcle)</option> + </param> + </when> + <when value="taxonomy"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="proteinclusters_taxonomy">Taxonomy Links (proteinclusters_taxonomy)</option> + </param> + </when> + </conditional> + </when> + <when value="pcassay"> + <conditional name="db_to"> + <param name="db_select_to" type="select" label="To NCBI Database"> + <option value="books">Books (books)</option> + <option value="cdd">Conserved Domains (cdd)</option> + <option value="gene">Gene (gene)</option> + <option value="nuccore">Nucleotide (nuccore)</option> + <option value="omim">OMIM (omim)</option> + <option value="pmc">PMC (pmc)</option> + <option value="protein">Protein (protein)</option> + <option value="pcassay">PubChem BioAssay (pcassay)</option> + <option value="pccompound">PubChem Compound (pccompound)</option> + <option value="pcsubstance">PubChem Substance (pcsubstance)</option> + <option value="pubmed">PubMed (pubmed)</option> + <option value="sparcle">Sparcle (sparcle)</option> + <option value="structure">Structure (structure)</option> + <option value="taxonomy">Taxonomy (taxonomy)</option> + </param> + <when value="books"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="pcassay_books_probe">MLP Chemical Probe Report (pcassay_books_probe)</option> + </param> + </when> + <when value="cdd"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="pcassay_cdd_protein_target">Conserved Domains (Full) via Protein Target (pcassay_cdd_protein_target)</option> + </param> + </when> + <when value="gene"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="pcassay_gene_target">Gene Target (pcassay_gene_target)</option> + <option value="pcassay_gene_rnai_active">RNAi Target, Active (pcassay_gene_rnai_active)</option> + <option value="pcassay_gene_rnai">RNAi Target, Tested (pcassay_gene_rnai)</option> + </param> + </when> + <when value="nuccore"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="pcassay_nuccore">Nucleotide (pcassay_nuccore)</option> + <option value="pcassay_nuccore_rna_target">Nucleotide RNA Target (pcassay_nuccore_rna_target)</option> + </param> + </when> + <when value="omim"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="pcassay_omim">OMIM (pcassay_omim)</option> + </param> + </when> + <when value="pmc"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="pcassay_pmc">PMC Articles (pcassay_pmc)</option> + </param> + </when> + <when value="protein"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="pcassay_protein_target">Protein Target (pcassay_protein_target)</option> + <option value="pcassay_protein_target_pig">Protein Target, Identical Sequence (pcassay_protein_target_pig)</option> + </param> + </when> + <when value="pcassay"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="pcassay_pcassay_assay_project">Related Assay Projects (pcassay_pcassay_assay_project)</option> + <option value="pcassay_pcassay_activityneighbor_list">Related BioAssays, by Activity Overlap (List) (pcassay_pcassay_activityneighbor_list)</option> + <option value="pcassay_pcassay_common_gene_list">Related BioAssays, by Common Active Gene (List) (pcassay_pcassay_common_gene_list)</option> + <option value="pcassay_pcassay_neighbor_list">Related BioAssays, by Depositor (List) (pcassay_pcassay_neighbor_list)</option> + <option value="pcassay_pcassay_gene_interaction_list">Related BioAssays, by Gene Interaction (List) (pcassay_pcassay_gene_interaction_list)</option> + <option value="pcassay_pcassay_same_assay_project_list">Related BioAssays, by Same Project (List) (pcassay_pcassay_same_assay_project_list)</option> + <option value="pcassay_pcassay_same_publication_list">Related BioAssays, by Same Publication (List) (pcassay_pcassay_same_publication_list)</option> + <option value="pcassay_pcassay_similar_publication_list">Related BioAssays, by Similar Publication (List) (pcassay_pcassay_similar_publication_list)</option> + <option value="pcassay_pcassay_targetneighbor_list">Related BioAssays, by Target Similarity (List) (pcassay_pcassay_targetneighbor_list)</option> + </param> + </when> + <when value="pccompound"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="pcassay_pccompound">Compounds (pcassay_pccompound)</option> + <option value="pcassay_pccompound_active">Compounds, Active (pcassay_pccompound_active)</option> + <option value="pcassay_pccompound_inactive">Compounds, Inactive (pcassay_pccompound_inactive)</option> + <option value="pcassay_pccompound_probe">Compounds, Probe (pcassay_pccompound_probe)</option> + <option value="pcassay_pccompound_activityconcnanomolar">Compounds, activity concentration at/below 1 nM (pcassay_pccompound_activityconcnanomolar)</option> + <option value="pcassay_pccompound_activityconcmicromolar">Compounds, activity concentration at/below 1 uM (pcassay_pccompound_activityconcmicromolar)</option> + </param> + </when> + <when value="pcsubstance"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="pcassay_pcsubstance">Substances (pcassay_pcsubstance)</option> + <option value="pcassay_pcsubstance_active">Substances, Active (pcassay_pcsubstance_active)</option> + <option value="pcassay_pcsubstance_inactive">Substances, Inactive (pcassay_pcsubstance_inactive)</option> + <option value="pcassay_pcsubstance_probe">Substances, Probe (pcassay_pcsubstance_probe)</option> + <option value="pcassay_pcsubstance_activityconcnanomolar">Substances, activity concentration at/below 1 nM (pcassay_pcsubstance_activityconcnanomolar)</option> + <option value="pcassay_pcsubstance_activityconcmicromolar">Substances, activity concentration at/below 1 uM (pcassay_pcsubstance_activityconcmicromolar)</option> + </param> + </when> + <when value="pubmed"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="pcassay_pubmed">PubMed Citations (pcassay_pubmed)</option> + </param> + </when> + <when value="sparcle"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="pcassay_sparcle_target">Target Functional Class (pcassay_sparcle_target)</option> + </param> + </when> + <when value="structure"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="pcassay_structure">Protein Structures (pcassay_structure)</option> + </param> + </when> + <when value="taxonomy"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="pcassay_taxonomy">Taxonomy (pcassay_taxonomy)</option> + </param> + </when> + </conditional> + </when> + <when value="pccompound"> + <conditional name="db_to"> + <param name="db_select_to" type="select" label="To NCBI Database"> + <option value="biosystems">BioSystems (biosystems)</option> + <option value="gene">Gene (gene)</option> + <option value="mesh">MeSH (mesh)</option> + <option value="nuccore">Nucleotide (nuccore)</option> + <option value="omim">OMIM (omim)</option> + <option value="pmc">PMC (pmc)</option> + <option value="protein">Protein (protein)</option> + <option value="pcassay">PubChem BioAssay (pcassay)</option> + <option value="pccompound">PubChem Compound (pccompound)</option> + <option value="pcsubstance">PubChem Substance (pcsubstance)</option> + <option value="pubmed">PubMed (pubmed)</option> + <option value="structure">Structure (structure)</option> + <option value="taxonomy">Taxonomy (taxonomy)</option> + </param> + <when value="biosystems"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="pccompound_biosystems">BioSystems (pccompound_biosystems)</option> + </param> + </when> + <when value="gene"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="pccompound_gene">Gene (pccompound_gene)</option> + </param> + </when> + <when value="mesh"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="pccompound_mesh">MeSH Keyword (pccompound_mesh)</option> + </param> + </when> + <when value="nuccore"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="pccompound_nuccore">Nucleotide Sequences (pccompound_nuccore)</option> + </param> + </when> + <when value="omim"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="pccompound_omim">OMIM (pccompound_omim)</option> + </param> + </when> + <when value="pmc"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="pccompound_pmc">PMC Articles (pccompound_pmc)</option> + </param> + </when> + <when value="protein"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="pccompound_protein">Protein Sequences (pccompound_protein)</option> + </param> + </when> + <when value="pcassay"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="pccompound_pcassay">BioAssays (pccompound_pcassay)</option> + <option value="pccompound_pcassay_active">BioAssays, Active (pccompound_pcassay_active)</option> + <option value="pccompound_pcassay_inactive">BioAssays, Inactive (pccompound_pcassay_inactive)</option> + <option value="pccompound_pcassay_probe">BioAssays, Probe (pccompound_pcassay_probe)</option> + <option value="pccompound_pcassay_activityconcnanomolar">BioAssays, activity concentration at/below 1 nM (pccompound_pcassay_activityconcnanomolar)</option> + <option value="pccompound_pcassay_activityconcmicromolar">BioAssays, activity concentration at/below 1 uM (pccompound_pcassay_activityconcmicromolar)</option> + </param> + </when> + <when value="pccompound"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="pccompound_pccompound_mixture">Mixture/Component Compounds (pccompound_pccompound_mixture)</option> + <option value="pccompound_pccompound_parent">Parent Compound (pccompound_pccompound_parent)</option> + <option value="pccompound_pccompound_parent_pulldown">Same Parent (pccompound_pccompound_parent_pulldown)</option> + <option value="pccompound_pccompound_parent_tautomer_pulldown">Same Parent, Any Tautomer (pccompound_pccompound_parent_tautomer_pulldown)</option> + <option value="pccompound_pccompound_parent_connectivity_pulldown">Same Parent, Connectivity (pccompound_pccompound_parent_connectivity_pulldown)</option> + <option value="pccompound_pccompound_parent_isotopes_pulldown">Same Parent, Isotopes (pccompound_pccompound_parent_isotopes_pulldown)</option> + <option value="pccompound_pccompound_parent_stereo_pulldown">Same Parent, Stereochemistry (pccompound_pccompound_parent_stereo_pulldown)</option> + <option value="pccompound_pccompound_sameanytautomer_pulldown">Same, Any Tautomer (pccompound_pccompound_sameanytautomer_pulldown)</option> + <option value="pccompound_pccompound_sameconnectivity_pulldown">Same, Connectivity (pccompound_pccompound_sameconnectivity_pulldown)</option> + <option value="pccompound_pccompound_sameisotopic_pulldown">Same, Isotopes (pccompound_pccompound_sameisotopic_pulldown)</option> + <option value="pccompound_pccompound_samestereochem_pulldown">Same, Stereochemistry (pccompound_pccompound_samestereochem_pulldown)</option> + <option value="pccompound_pccompound">Similar Compounds (pccompound_pccompound)</option> + <option value="pccompound_pccompound_3d">Similar Conformers (pccompound_pccompound_3d)</option> + </param> + </when> + <when value="pcsubstance"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="pccompound_pcsubstance">PubChem Mixture Substances (pccompound_pcsubstance)</option> + <option value="pccompound_pcsubstance_same">PubChem Same Substances (pccompound_pcsubstance_same)</option> + </param> + </when> + <when value="pubmed"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="pccompound_pubmed_mesh">PubMed (MeSH Keyword) (pccompound_pubmed_mesh)</option> + <option value="pccompound_pubmed_publisher">PubMed (Publisher) (pccompound_pubmed_publisher)</option> + <option value="pccompound_pubmed">PubMed Citations (pccompound_pubmed)</option> + </param> + </when> + <when value="structure"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="pccompound_structure">Protein Structures (pccompound_structure)</option> + </param> + </when> + <when value="taxonomy"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="pccompound_taxonomy">Taxonomy (pccompound_taxonomy)</option> + </param> + </when> + </conditional> + </when> + <when value="pcsubstance"> + <conditional name="db_to"> + <param name="db_select_to" type="select" label="To NCBI Database"> + <option value="biosystems">BioSystems (biosystems)</option> + <option value="books">Books (books)</option> + <option value="gene">Gene (gene)</option> + <option value="nuccore">Nucleotide (nuccore)</option> + <option value="omim">OMIM (omim)</option> + <option value="pmc">PMC (pmc)</option> + <option value="protein">Protein (protein)</option> + <option value="pcassay">PubChem BioAssay (pcassay)</option> + <option value="pccompound">PubChem Compound (pccompound)</option> + <option value="pubmed">PubMed (pubmed)</option> + <option value="structure">Structure (structure)</option> + <option value="taxonomy">Taxonomy (taxonomy)</option> + </param> + <when value="biosystems"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="pcsubstance_biosystems">BioSystems (pcsubstance_biosystems)</option> + </param> + </when> + <when value="books"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="pcsubstance_books">Books (pcsubstance_books)</option> + </param> + </when> + <when value="gene"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="pcsubstance_gene">Gene (pcsubstance_gene)</option> + </param> + </when> + <when value="nuccore"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="pcsubstance_nuccore">Nucleotide Sequences (pcsubstance_nuccore)</option> + </param> + </when> + <when value="omim"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="pcsubstance_omim">OMIM (pcsubstance_omim)</option> + </param> + </when> + <when value="pmc"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="pcsubstance_pmc">PMC Articles (pcsubstance_pmc)</option> + </param> + </when> + <when value="protein"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="pcsubstance_protein">Protein Sequences (pcsubstance_protein)</option> + </param> + </when> + <when value="pcassay"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="pcsubstance_pcassay">BioAssays (pcsubstance_pcassay)</option> + <option value="pcsubstance_pcassay_active">BioAssays, Active (pcsubstance_pcassay_active)</option> + <option value="pcsubstance_pcassay_inactive">BioAssays, Inactive (pcsubstance_pcassay_inactive)</option> + <option value="pcsubstance_pcassay_probe">BioAssays, Probe (pcsubstance_pcassay_probe)</option> + <option value="pcsubstance_pcassay_activityconcnanomolar">BioAssays, activity concentration at/below 1 nM (pcsubstance_pcassay_activityconcnanomolar)</option> + <option value="pcsubstance_pcassay_activityconcmicromolar">BioAssays, activity concentration at/below 1 uM (pcsubstance_pcassay_activityconcmicromolar)</option> + </param> + </when> + <when value="pccompound"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="pcsubstance_pccompound">PubChem Component Compounds (pcsubstance_pccompound)</option> + <option value="pcsubstance_pccompound_same">PubChem Same Compounds (pcsubstance_pccompound_same)</option> + </param> + </when> + <when value="pubmed"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="pcsubstance_pubmed_bookrecords">"Bookshelf (from PubChem Substance)" (pcsubstance_pubmed_bookrecords)</option> + <option value="pcsubstance_pubmed_publisher">PubMed (Publisher) (pcsubstance_pubmed_publisher)</option> + <option value="pcsubstance_pubmed">PubMed Citations (pcsubstance_pubmed)</option> + </param> + </when> + <when value="structure"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="pcsubstance_structure">Protein Structures (pcsubstance_structure)</option> + </param> + </when> + <when value="taxonomy"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="pcsubstance_taxonomy">Taxonomy (pcsubstance_taxonomy)</option> + </param> + </when> + </conditional> + </when> + <when value="pubmed"> + <conditional name="db_to"> + <param name="db_select_to" type="select" label="To NCBI Database"> + <option value="assembly">Assembly (assembly)</option> + <option value="bioproject">BioProject (bioproject)</option> + <option value="biosample">BioSample (biosample)</option> + <option value="biosystems">BioSystems (biosystems)</option> + <option value="books">Books (books)</option> + <option value="clinvar">ClinVar (clinvar)</option> + <option value="cdd">Conserved Domains (cdd)</option> + <option value="gds">GEO DataSets (gds)</option> + <option value="geoprofiles">GEO Profiles (geoprofiles)</option> + <option value="gene">Gene (gene)</option> + <option value="genome">Genome (genome)</option> + <option value="homologene">HomoloGene (homologene)</option> + <option value="medgen">MedGen (medgen)</option> + <option value="nuccore">Nucleotide (nuccore)</option> + <option value="omim">OMIM (omim)</option> + <option value="pmc">PMC (pmc)</option> + <option value="popset">PopSet (popset)</option> + <option value="protein">Protein (protein)</option> + <option value="proteinclusters">Protein Clusters (proteinclusters)</option> + <option value="pcassay">PubChem BioAssay (pcassay)</option> + <option value="pccompound">PubChem Compound (pccompound)</option> + <option value="pcsubstance">PubChem Substance (pcsubstance)</option> + <option value="pubmed">PubMed (pubmed)</option> + <option value="snp">SNP (snp)</option> + <option value="sra">SRA (sra)</option> + <option value="structure">Structure (structure)</option> + <option value="taxonomy">Taxonomy (taxonomy)</option> + <option value="gap">dbGaP (gap)</option> + <option value="dbvar">dbVar (dbvar)</option> + </param> + <when value="assembly"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="pubmed_assembly">Assembly (pubmed_assembly)</option> + </param> + </when> + <when value="bioproject"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="pubmed_bioproject">Project Links (pubmed_bioproject)</option> + </param> + </when> + <when value="biosample"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="pubmed_biosample">BioSample Links (pubmed_biosample)</option> + </param> + </when> + <when value="biosystems"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="pubmed_biosystems">BioSystem Links (pubmed_biosystems)</option> + </param> + </when> + <when value="books"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="pubmed_books_refs">Cited in Books (pubmed_books_refs)</option> + </param> + </when> + <when value="clinvar"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="pubmed_clinvar_calculated">ClinVar (calculated) (pubmed_clinvar_calculated)</option> + <option value="pubmed_clinvar">ClinVar (pubmed_clinvar)</option> + </param> + </when> + <when value="cdd"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="pubmed_cdd">Conserved Domain Links (pubmed_cdd)</option> + </param> + </when> + <when value="gds"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="pubmed_gds">GEO DataSet Links (pubmed_gds)</option> + </param> + </when> + <when value="geoprofiles"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="pubmed_geoprofiles">GEO Profile Links (pubmed_geoprofiles)</option> + </param> + </when> + <when value="gene"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="pubmed_gene_rif">Gene (GeneRIF) Links (pubmed_gene_rif)</option> + <option value="pubmed_gene_citedinomim">Gene (OMIM) Links (pubmed_gene_citedinomim)</option> + <option value="pubmed_gene_bookrecords">Gene (from Bookshelf) (pubmed_gene_bookrecords)</option> + <option value="pubmed_gene_pmc_nucleotide">Gene (nucleotide/PMC) (pubmed_gene_pmc_nucleotide)</option> + <option value="pubmed_gene">Gene Links (pubmed_gene)</option> + </param> + </when> + <when value="genome"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="pubmed_genome">Genome Links (pubmed_genome)</option> + </param> + </when> + <when value="homologene"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="pubmed_homologene">HomoloGene Links (pubmed_homologene)</option> + </param> + </when> + <when value="medgen"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="pubmed_medgen_bookshelf_cited">MedGen (Bookshelf cited) (pubmed_medgen_bookshelf_cited)</option> + <option value="pubmed_medgen_genereviews">MedGen (GeneReviews) (pubmed_medgen_genereviews)</option> + <option value="pubmed_medgen_omim">MedGen (OMIM) (pubmed_medgen_omim)</option> + <option value="pubmed_medgen">MedGen (pubmed_medgen)</option> + </param> + </when> + <when value="nuccore"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="pubmed_nuccore_refseq">Nucleotide (RefSeq) Links (pubmed_nuccore_refseq)</option> + <option value="pubmed_nuccore_weighted">Nucleotide (Weighted) Links (pubmed_nuccore_weighted)</option> + <option value="pubmed_nuccore">Nucleotide Links (pubmed_nuccore)</option> + </param> + </when> + <when value="omim"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="pubmed_omim_calculated">OMIM (calculated) Links (pubmed_omim_calculated)</option> + <option value="pubmed_omim_cited">OMIM (cited) Links (pubmed_omim_cited)</option> + <option value="pubmed_omim_bookrecords">OMIM (from Bookshelf) (pubmed_omim_bookrecords)</option> + </param> + </when> + <when value="pmc"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="pubmed_pmc_embargo"> (pubmed_pmc_embargo)</option> + <option value="pubmed_pmc_local"> (pubmed_pmc_local)</option> + <option value="pubmed_pmc_refs">Cited in PMC (pubmed_pmc_refs)</option> + <option value="pubmed_pmc">PMC Links (pubmed_pmc)</option> + <option value="pubmed_pmc_bookrecords">References in PMC for this Bookshelf citation (pubmed_pmc_bookrecords)</option> + </param> + </when> + <when value="popset"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="pubmed_popset">PopSet Links (pubmed_popset)</option> + </param> + </when> + <when value="protein"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="pubmed_protein_refseq">Protein (RefSeq) Links (pubmed_protein_refseq)</option> + <option value="pubmed_protein_weighted">Protein (Weighted) Links (pubmed_protein_weighted)</option> + <option value="pubmed_protein">Protein Links (pubmed_protein)</option> + </param> + </when> + <when value="proteinclusters"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="pubmed_proteinclusters">Protein Cluster Links (pubmed_proteinclusters)</option> + </param> + </when> + <when value="pcassay"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="pubmed_pcassay">PubChem BioAssay (pubmed_pcassay)</option> + </param> + </when> + <when value="pccompound"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="pubmed_pccompound_mesh">PubChem Compound (MeSH Keyword) (pubmed_pccompound_mesh)</option> + <option value="pubmed_pccompound_publisher">PubChem Compound (Publisher) (pubmed_pccompound_publisher)</option> + <option value="pubmed_pccompound">PubChem Compound (pubmed_pccompound)</option> + </param> + </when> + <when value="pcsubstance"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="pubmed_pcsubstance_publisher">PubChem Substance (Publisher) (pubmed_pcsubstance_publisher)</option> + <option value="pubmed_pcsubstance_bookrecords">PubChem Substance (from Bookshelf) (pubmed_pcsubstance_bookrecords)</option> + <option value="pubmed_pcsubstance">PubChem Substance Links (pubmed_pcsubstance)</option> + </param> + </when> + <when value="pubmed"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="pubmed_pubmed_alsoviewed">Articles frequently viewed together (pubmed_pubmed_alsoviewed)</option> + <option value="pubmed_pubmed_refs">References for PMC Articles (pubmed_pubmed_refs)</option> + <option value="pubmed_pubmed_bookrecords">References for this Bookshelf citation (pubmed_pubmed_bookrecords)</option> + <option value="pubmed_pubmed">Similar articles (pubmed_pubmed)</option> + </param> + </when> + <when value="snp"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="pubmed_snp_cited">SNP (Cited) (pubmed_snp_cited)</option> + <option value="pubmed_snp">SNP Links (pubmed_snp)</option> + </param> + </when> + <when value="sra"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="pubmed_sra">SRA Links (pubmed_sra)</option> + </param> + </when> + <when value="structure"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="pubmed_structure">Structure Links (pubmed_structure)</option> + </param> + </when> + <when value="taxonomy"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="pubmed_taxonomy_entrez">Taxonomy via GenBank (pubmed_taxonomy_entrez)</option> + </param> + </when> + <when value="gap"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="pubmed_gap">dbGaP Links (pubmed_gap)</option> + </param> + </when> + <when value="dbvar"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="pubmed_dbvar">dbVar (pubmed_dbvar)</option> + </param> + </when> + </conditional> + </when> + <when value="snp"> + <conditional name="db_to"> + <param name="db_select_to" type="select" label="To NCBI Database"> + <option value="bioproject">BioProject (bioproject)</option> + <option value="biosample">BioSample (biosample)</option> + <option value="clinvar">ClinVar (clinvar)</option> + <option value="gene">Gene (gene)</option> + <option value="nuccore">Nucleotide (nuccore)</option> + <option value="pmc">PMC (pmc)</option> + <option value="protein">Protein (protein)</option> + <option value="pubmed">PubMed (pubmed)</option> + <option value="snp">SNP (snp)</option> + <option value="sparcle">Sparcle (sparcle)</option> + <option value="structure">Structure (structure)</option> + <option value="taxonomy">Taxonomy (taxonomy)</option> + <option value="gap">dbGaP (gap)</option> + <option value="dbvar">dbVar (dbvar)</option> + </param> + <when value="bioproject"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="snp_bioproject">BioProject Links (snp_bioproject)</option> + </param> + </when> + <when value="biosample"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="snp_biosample">BioSample Links (snp_biosample)</option> + </param> + </when> + <when value="clinvar"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="snp_clinvar">ClinVar (snp_clinvar)</option> + </param> + </when> + <when value="gene"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="snp_gene">Gene Links (snp_gene)</option> + </param> + </when> + <when value="nuccore"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="snp_nuccore">Nucleotide Links (snp_nuccore)</option> + </param> + </when> + <when value="pmc"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="snp_pmc">PMC Links (snp_pmc)</option> + </param> + </when> + <when value="protein"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="snp_protein">Protein Links (snp_protein)</option> + </param> + </when> + <when value="pubmed"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="snp_pubmed">PubMed Links (snp_pubmed)</option> + <option value="snp_pubmed_cited">Pubmed (SNP Cited) (snp_pubmed_cited)</option> + </param> + </when> + <when value="snp"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="snp_snp_genegenotype">Gene Genotype Links (snp_snp_genegenotype)</option> + <option value="snp_snp_somatic">Somatic SNPs (snp_snp_somatic)</option> + </param> + </when> + <when value="sparcle"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="snp_sparcle">Functional Class (snp_sparcle)</option> + </param> + </when> + <when value="structure"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="snp_structure">Structure Links (snp_structure)</option> + </param> + </when> + <when value="taxonomy"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="snp_taxonomy">Taxonomy Links (snp_taxonomy)</option> + </param> + </when> + <when value="gap"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="snp_gap">GAP Links (snp_gap)</option> + </param> + </when> + <when value="dbvar"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="snp_dbvar">dbVar (snp_dbvar)</option> + </param> + </when> + </conditional> + </when> + <when value="sra"> + <conditional name="db_to"> + <param name="db_select_to" type="select" label="To NCBI Database"> + <option value="assembly">Assembly (assembly)</option> + <option value="bioproject">BioProject (bioproject)</option> + <option value="biosample">BioSample (biosample)</option> + <option value="gds">GEO DataSets (gds)</option> + <option value="genome">Genome (genome)</option> + <option value="nuccore">Nucleotide (nuccore)</option> + <option value="omim">OMIM (omim)</option> + <option value="pmc">PMC (pmc)</option> + <option value="pubmed">PubMed (pubmed)</option> + <option value="taxonomy">Taxonomy (taxonomy)</option> + <option value="gap">dbGaP (gap)</option> + </param> + <when value="assembly"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="sra_assembly">Assembly Links (sra_assembly)</option> + </param> + </when> + <when value="bioproject"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="sra_bioproject">BioProject Links (sra_bioproject)</option> + <option value="sra_bioproject_sp">bioproject (sra_bioproject_sp)</option> + </param> + </when> + <when value="biosample"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="sra_biosample">BioSample Links (sra_biosample)</option> + </param> + </when> + <when value="gds"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="sra_gds">GEO DataSet Links (sra_gds)</option> + </param> + </when> + <when value="genome"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="sra_genome">genome (sra_genome)</option> + </param> + </when> + <when value="nuccore"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="sra_nuccore">Nucleotide Links (sra_nuccore)</option> + <option value="sra_nuccore_wgs">WGS links (sra_nuccore_wgs)</option> + </param> + </when> + <when value="omim"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="sra_omim">Omim links (sra_omim)</option> + </param> + </when> + <when value="pmc"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="sra_pmc">PMC (sra_pmc)</option> + </param> + </when> + <when value="pubmed"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="sra_pubmed">PubMed Links (sra_pubmed)</option> + </param> + </when> + <when value="taxonomy"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="sra_taxonomy">Taxonomy Links (sra_taxonomy)</option> + </param> + </when> + <when value="gap"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="sra_gap_all">dbGaP Links (sra_gap_all)</option> + </param> + </when> + </conditional> + </when> + <when value="seqannot"> + <conditional name="db_to"> + <param name="db_select_to" type="select" label="To NCBI Database"> + <option value="bioproject">BioProject (bioproject)</option> + <option value="nuccore">Nucleotide (nuccore)</option> + </param> + <when value="bioproject"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="seqannot_bioproject">BioProject links (seqannot_bioproject)</option> + </param> + </when> + <when value="nuccore"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="seqannot_nuccore">NucCore links (seqannot_nuccore)</option> + </param> + </when> + </conditional> + </when> + <when value="sparcle"> + <conditional name="db_to"> + <param name="db_select_to" type="select" label="To NCBI Database"> + <option value="biosystems">BioSystems (biosystems)</option> + <option value="clinvar">ClinVar (clinvar)</option> + <option value="cdd">Conserved Domains (cdd)</option> + <option value="geoprofiles">GEO Profiles (geoprofiles)</option> + <option value="gtr">GTR (gtr)</option> + <option value="gene">Gene (gene)</option> + <option value="homologene">HomoloGene (homologene)</option> + <option value="medgen">MedGen (medgen)</option> + <option value="nuccore">Nucleotide (nuccore)</option> + <option value="omim">OMIM (omim)</option> + <option value="protein">Protein (protein)</option> + <option value="proteinclusters">Protein Clusters (proteinclusters)</option> + <option value="pcassay">PubChem BioAssay (pcassay)</option> + <option value="snp">SNP (snp)</option> + <option value="structure">Structure (structure)</option> + <option value="dbvar">dbVar (dbvar)</option> + </param> + <when value="biosystems"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="sparcle_biosystems">Pathways (sparcle_biosystems)</option> + </param> + </when> + <when value="clinvar"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="sparcle_clinvar">Clinical Variants (sparcle_clinvar)</option> + </param> + </when> + <when value="cdd"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="sparcle_cdd">Domains (sparcle_cdd)</option> + </param> + </when> + <when value="geoprofiles"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="sparcle_geoprofiles">Microarray (sparcle_geoprofiles)</option> + </param> + </when> + <when value="gtr"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="sparcle_gtr">Gene Tests (sparcle_gtr)</option> + </param> + </when> + <when value="gene"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="sparcle_gene">Genes (sparcle_gene)</option> + </param> + </when> + <when value="homologene"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="sparcle_homologene">Homologene (sparcle_homologene)</option> + </param> + </when> + <when value="medgen"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="sparcle_medgen_diseases">Genetic diseases (sparcle_medgen_diseases)</option> + </param> + </when> + <when value="nuccore"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="sparcle_nuccore_mrna">mRNAs (sparcle_nuccore_mrna)</option> + </param> + </when> + <when value="omim"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="sparcle_omim">OMIM (sparcle_omim)</option> + </param> + </when> + <when value="protein"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="sparcle_protein">Proteins (sparcle_protein)</option> + </param> + </when> + <when value="proteinclusters"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="sparcle_proteinclusters">Protein Clusters (sparcle_proteinclusters)</option> + </param> + </when> + <when value="pcassay"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="sparcle_pcassay_target">BioAssays (sparcle_pcassay_target)</option> + </param> + </when> + <when value="snp"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="sparcle_snp">SNPs (sparcle_snp)</option> + </param> + </when> + <when value="structure"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="sparcle_structure">3D Structures (sparcle_structure)</option> + </param> + </when> + <when value="dbvar"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="sparcle_dbvar">Variants (sparcle_dbvar)</option> + </param> + </when> + </conditional> + </when> + <when value="structure"> + <conditional name="db_to"> + <param name="db_select_to" type="select" label="To NCBI Database"> + <option value="biosystems">BioSystems (biosystems)</option> + <option value="cdd">Conserved Domains (cdd)</option> + <option value="gene">Gene (gene)</option> + <option value="nuccore">Nucleotide (nuccore)</option> + <option value="omim">OMIM (omim)</option> + <option value="pmc">PMC (pmc)</option> + <option value="protein">Protein (protein)</option> + <option value="pcassay">PubChem BioAssay (pcassay)</option> + <option value="pccompound">PubChem Compound (pccompound)</option> + <option value="pcsubstance">PubChem Substance (pcsubstance)</option> + <option value="pubmed">PubMed (pubmed)</option> + <option value="snp">SNP (snp)</option> + <option value="sparcle">Sparcle (sparcle)</option> + <option value="structure">Structure (structure)</option> + <option value="taxonomy">Taxonomy (taxonomy)</option> + </param> + <when value="biosystems"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="structure_biosystems">BioSystem Links (structure_biosystems)</option> + </param> + </when> + <when value="cdd"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="structure_cdd_family_2">Conserved Domain Family Links (structure_cdd_family_2)</option> + <option value="structure_cdd">Conserved Domain Links (structure_cdd)</option> + <option value="structure_cdd_superfamily_2">Conserved Domain Superfamily Links (structure_cdd_superfamily_2)</option> + </param> + </when> + <when value="gene"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="structure_gene">Gene (structure_gene)</option> + </param> + </when> + <when value="nuccore"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="structure_nuccore">Nucleotide Links (structure_nuccore)</option> + </param> + </when> + <when value="omim"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="structure_omim">OMIM Links (structure_omim)</option> + </param> + </when> + <when value="pmc"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="structure_pmc">PMC Links (structure_pmc)</option> + </param> + </when> + <when value="protein"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="structure_protein">Identical Proteins (structure_protein)</option> + <option value="structure_protein_direct">Proteins (structure_protein_direct)</option> + <option value="structure_protein_related_list">Related Proteins (structure_protein_related_list)</option> + </param> + </when> + <when value="pcassay"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="structure_pcassay">BioAssay Links (structure_pcassay)</option> + </param> + </when> + <when value="pccompound"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="structure_pccompound">PubChem Compound Links (structure_pccompound)</option> + </param> + </when> + <when value="pcsubstance"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="structure_pcsubstance">PubChem Substance Links (structure_pcsubstance)</option> + </param> + </when> + <when value="pubmed"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="structure_pubmed">PubMed Links (structure_pubmed)</option> + </param> + </when> + <when value="snp"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="structure_snp">SNP Links (structure_snp)</option> + </param> + </when> + <when value="sparcle"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="structure_sparcle">Functional Class (structure_sparcle)</option> + </param> + </when> + <when value="structure"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="structure_mmdb">Related Structures (structure_mmdb)</option> + </param> + </when> + <when value="taxonomy"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="structure_taxonomy">Taxonomy Links (structure_taxonomy)</option> + </param> + </when> + </conditional> + </when> + <when value="taxonomy"> + <conditional name="db_to"> + <param name="db_select_to" type="select" label="To NCBI Database"> + <option value="assembly">Assembly (assembly)</option> + <option value="bioproject">BioProject (bioproject)</option> + <option value="biosample">BioSample (biosample)</option> + <option value="biosystems">BioSystems (biosystems)</option> + <option value="books">Books (books)</option> + <option value="cdd">Conserved Domains (cdd)</option> + <option value="gds">GEO DataSets (gds)</option> + <option value="geoprofiles">GEO Profiles (geoprofiles)</option> + <option value="gene">Gene (gene)</option> + <option value="genome">Genome (genome)</option> + <option value="homologene">HomoloGene (homologene)</option> + <option value="mesh">MeSH (mesh)</option> + <option value="nuccore">Nucleotide (nuccore)</option> + <option value="pmc">PMC (pmc)</option> + <option value="popset">PopSet (popset)</option> + <option value="protein">Protein (protein)</option> + <option value="proteinclusters">Protein Clusters (proteinclusters)</option> + <option value="pcassay">PubChem BioAssay (pcassay)</option> + <option value="pccompound">PubChem Compound (pccompound)</option> + <option value="pcsubstance">PubChem Substance (pcsubstance)</option> + <option value="pubmed">PubMed (pubmed)</option> + <option value="snp">SNP (snp)</option> + <option value="sra">SRA (sra)</option> + <option value="structure">Structure (structure)</option> + <option value="dbvar">dbVar (dbvar)</option> + </param> + <when value="assembly"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="taxonomy_assembly_exp">Assembly Links (taxonomy_assembly_exp)</option> + </param> + </when> + <when value="bioproject"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="taxonomy_bioproject_exp">BioProject Links (taxonomy_bioproject_exp)</option> + </param> + </when> + <when value="biosample"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="taxonomy_biosample_exp">BioSample Links (taxonomy_biosample_exp)</option> + </param> + </when> + <when value="biosystems"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="taxonomy_biosystems_exp">Biosystems Links (taxonomy_biosystems_exp)</option> + </param> + </when> + <when value="books"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="taxonomy_books">Books Links (taxonomy_books)</option> + </param> + </when> + <when value="cdd"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="taxonomy_cdd_exp">Conserved Domain Links (taxonomy_cdd_exp)</option> + </param> + </when> + <when value="gds"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="taxonomy_gds_exp">GEO DataSet Links (taxonomy_gds_exp)</option> + </param> + </when> + <when value="geoprofiles"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="taxonomy_geoprofiles"> (taxonomy_geoprofiles)</option> + </param> + </when> + <when value="gene"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="taxonomy_gene_exp">Gene Links (taxonomy_gene_exp)</option> + </param> + </when> + <when value="genome"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="taxonomy_genome">Genome Links (taxonomy_genome)</option> + </param> + </when> + <when value="homologene"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="taxonomy_homologene_exp">HomoloGene Links (taxonomy_homologene_exp)</option> + </param> + </when> + <when value="mesh"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="taxonomy_mesh">MeSH Links (taxonomy_mesh)</option> + </param> + </when> + <when value="nuccore"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="taxonomy_nucleotide_exp">Nucleotide Links (taxonomy_nucleotide_exp)</option> + </param> + </when> + <when value="pmc"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="taxonomy_pmc">PMC Links (taxonomy_pmc)</option> + </param> + </when> + <when value="popset"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="taxonomy_popset">PopSet Links (taxonomy_popset)</option> + </param> + </when> + <when value="protein"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="taxonomy_protein_species2wp">Links from species level taxonomic nodes to autonomous proteins (taxonomy_protein_species2wp)</option> + <option value="taxonomy_protein_exp">Protein Links (taxonomy_protein_exp)</option> + </param> + </when> + <when value="proteinclusters"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="taxonomy_proteinclusters_exp">Protein Clusters Links (taxonomy_proteinclusters_exp)</option> + </param> + </when> + <when value="pcassay"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="taxonomy_pcassay">PubChem BioAssay Links (taxonomy_pcassay)</option> + </param> + </when> + <when value="pccompound"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="taxonomy_pccompound">PubChem Compound Links (taxonomy_pccompound)</option> + </param> + </when> + <when value="pcsubstance"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="taxonomy_pcsubstance">PubChem Substance Links (taxonomy_pcsubstance)</option> + </param> + </when> + <when value="pubmed"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="taxonomy_pubmed">PubMed Links (taxonomy_pubmed)</option> + <option value="taxonomy_pubmed_entrez">PubMed via GenBank (taxonomy_pubmed_entrez)</option> + </param> + </when> + <when value="snp"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="taxonomy_snp_exp">SNP Links (taxonomy_snp_exp)</option> + </param> + </when> + <when value="sra"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="taxonomy_sra_exp">SRA Links (taxonomy_sra_exp)</option> + </param> + </when> + <when value="structure"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="taxonomy_structure_exp">Structure Links (taxonomy_structure_exp)</option> + </param> + </when> + <when value="dbvar"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="taxonomy_dbvar_exp">dbVar Links (taxonomy_dbvar_exp)</option> + </param> + </when> + </conditional> + </when> + <when value="gap"> + <conditional name="db_to"> + <param name="db_select_to" type="select" label="To NCBI Database"> + <option value="bioproject">BioProject (bioproject)</option> + <option value="biosample">BioSample (biosample)</option> + <option value="gds">GEO DataSets (gds)</option> + <option value="gene">Gene (gene)</option> + <option value="mesh">MeSH (mesh)</option> + <option value="medgen">MedGen (medgen)</option> + <option value="pmc">PMC (pmc)</option> + <option value="pubmed">PubMed (pubmed)</option> + <option value="snp">SNP (snp)</option> + <option value="sra">SRA (sra)</option> + <option value="dbvar">dbVar (dbvar)</option> + </param> + <when value="bioproject"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="gap_bioproject">BioProject Links (gap_bioproject)</option> + </param> + </when> + <when value="biosample"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="gap_biosample_all">BioSample Links (gap_biosample_all)</option> + </param> + </when> + <when value="gds"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="gap_gds">GEO DataSets (gap_gds)</option> + </param> + </when> + <when value="gene"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="gap_gene">Gene Links (gap_gene)</option> + </param> + </when> + <when value="mesh"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="gap_mesh">MeSH (gap_mesh)</option> + </param> + </when> + <when value="medgen"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="gap_medgen">MedGen (gap_medgen)</option> + </param> + </when> + <when value="pmc"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="gap_pmc">PMC Links (gap_pmc)</option> + </param> + </when> + <when value="pubmed"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="gap_pubmed">PubMed Links (gap_pubmed)</option> + </param> + </when> + <when value="snp"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="gap_snp">SNP Links (gap_snp)</option> + </param> + </when> + <when value="sra"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="gap_sra_all">SRA Links (gap_sra_all)</option> + </param> + </when> + <when value="dbvar"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="gap_dbvar">dbVar (gap_dbvar)</option> + </param> + </when> + </conditional> + </when> + <when value="dbvar"> + <conditional name="db_to"> + <param name="db_select_to" type="select" label="To NCBI Database"> + <option value="bioproject">BioProject (bioproject)</option> + <option value="biosample">BioSample (biosample)</option> + <option value="biosystems">BioSystems (biosystems)</option> + <option value="clinvar">ClinVar (clinvar)</option> + <option value="gds">GEO DataSets (gds)</option> + <option value="gene">Gene (gene)</option> + <option value="nuccore">Nucleotide (nuccore)</option> + <option value="omim">OMIM (omim)</option> + <option value="pubmed">PubMed (pubmed)</option> + <option value="snp">SNP (snp)</option> + <option value="sparcle">Sparcle (sparcle)</option> + <option value="taxonomy">Taxonomy (taxonomy)</option> + <option value="gap">dbGaP (gap)</option> + </param> + <when value="bioproject"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="dbvar_bioproject">BioProjects Links (dbvar_bioproject)</option> + </param> + </when> + <when value="biosample"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="dbvar_biosample">BioSample Links (dbvar_biosample)</option> + </param> + </when> + <when value="biosystems"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="dbvar_biosystems_gene">Pathways + GO (dbvar_biosystems_gene)</option> + </param> + </when> + <when value="clinvar"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="dbvar_clinvar">ClinVar (dbvar_clinvar)</option> + </param> + </when> + <when value="gds"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="dbvar_gds">GEO DataSets Links (dbvar_gds)</option> + </param> + </when> + <when value="gene"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="dbvar_gene">Gene Links (dbvar_gene)</option> + </param> + </when> + <when value="nuccore"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="dbvar_nuccore">Nucleotide Links (dbvar_nuccore)</option> + </param> + </when> + <when value="omim"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="dbvar_omim">OMIM Links (dbvar_omim)</option> + </param> + </when> + <when value="pubmed"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="dbvar_pubmed">PubMed Links (dbvar_pubmed)</option> + </param> + </when> + <when value="snp"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="dbvar_snp">dbSNP Links (dbvar_snp)</option> + </param> + </when> + <when value="sparcle"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="dbvar_sparcle">Functional Class (dbvar_sparcle)</option> + </param> + </when> + <when value="taxonomy"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="dbvar_taxonomy">Taxonomy Links (dbvar_taxonomy)</option> + </param> + </when> + <when value="gap"> + <param name="linkname" type="select" label="Link Name"> + <option value="None">All Links</option> + <option value="dbvar_gap">dbGaP Links (dbvar_gap)</option> + </param> + </when> + </conditional> + </when> + <when value="grasp"> + <conditional name="db_to"> + <param name="db_select_to" type="select" label="To NCBI Database"> + <option value="grasp">grasp (grasp)</option> + </param> + <when value="grasp"> + <param name="linkname" type="select" label="Link Name"> + <option value="none">All Links</option> + </param> + </when> + </conditional> + </when> + <when value="annotinfo"> + <conditional name="db_to"> + <param name="db_select_to" type="select" label="To NCBI Database"> + <option value="none">Not applicable</option> + </param> + <when value="none"> + <param name="linkname" type="select" label="Link Name"> + <option value="none">Not applicable</option> + </param> + </when> + </conditional> + </when> + <when value="gapplus"> + <conditional name="db_to"> + <param name="db_select_to" type="select" label="To NCBI Database"> + <option value="none">Not applicable</option> + </param> + <when value="none"> + <param name="linkname" type="select" label="Link Name"> + <option value="none">Not applicable</option> + </param> + </when> + </conditional> + </when> + <when value="ncbisearch"> + <conditional name="db_to"> + <param name="db_select_to" type="select" label="To NCBI Database"> + <option value="none">Not applicable</option> + </param> + <when value="none"> + <param name="linkname" type="select" label="Link Name"> + <option value="none">Not applicable</option> + </param> + </when> + </conditional> + </when> + <when value="grasp"> + <conditional name="db_to"> + <param name="db_select_to" type="select" label="To NCBI Database"> + <option value="none">Not applicable</option> + </param> + <when value="none"> + <param name="linkname" type="select" label="Link Name"> + <option value="none">Not applicable</option> + </param> + </when> + </conditional> + </when> + </conditional> + </xml> + <token name="@LINK_TOKEN@"> + <![CDATA[ +#if $cmd.db_from_link.db_to.db_select_to == 'n/a': + none +#else: + $cmd.db_from_link.db_to.db_select_to +#end if + +$cmd.db_from_link.db_select_from_link + +$cmd.cmd_select + +#if $cmd.output_format == 'json': + --retmode json +#elif $cmd.output_format == 'text': + --retmode uilist +#else: + --retmode xml +#end if + +#if $cmd.db_from_link.db_to.linkname != 'None' and $cmd.cmd_select in ('neighbor', 'neighbor_history', 'neighbor_score'): + --linkname $cmd.db_from_link.db_to.linkname +#end if + ]]> + </token> </macros>