Mercurial > repos > iuc > ncbi_eutils_esummary
diff macros.xml @ 0:92bd8a680b9d draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
| author | iuc |
|---|---|
| date | Thu, 07 Jul 2016 02:41:02 -0400 |
| parents | |
| children | c8d4ea6376a7 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Thu Jul 07 02:41:02 2016 -0400 @@ -0,0 +1,847 @@ +<?xml version="1.0"?> +<macros> + <token name="@WRAPPER_VERSION@">1.1</token> + <token name="@EMAIL_ARGUMENTS@"> +--user_email "$__user_email__" +#set admin_emails = ';'.join(str($__admin_users__).split(',')) +--admin_email "$admin_emails" + </token> + <!-- TODO: citation --> + <token name="@REFERENCES@"><![CDATA[ + ]]></token> + <token name="@DISCLAIMER@"><![CDATA[ +Usage Guidelines and Requirements +================================= + +Frequency, Timing, and Registration of E-utility URL Requests +------------------------------------------------------------- + +In order not to overload the E-utility servers, NCBI recommends that users +limit large jobs to either weekends or between 9:00 PM and 5:00 AM Eastern time +during weekdays. Failure to comply with this policy may result in an IP address +being blocked from accessing NCBI. + +Minimizing the Number of Requests +--------------------------------- + +If a task requires searching for and/or downloading a large number of +records, it is much more efficient to use the Entrez History to upload +and/or retrieve these records in batches rather than using separate +requests for each record. Please refer to Application 3 in Chapter 3 +for an example. Many thousands of IDs can be uploaded using a single +EPost request, and several hundred records can be downloaded using one +EFetch request. + + +Disclaimer and Copyright Issues +------------------------------- + +In accordance with requirements of NCBI's E-Utilities, we must provide +the following disclaimer: + +Please note that abstracts in PubMed may incorporate material that may +be protected by U.S. and foreign copyright laws. All persons +reproducing, redistributing, or making commercial use of this +information are expected to adhere to the terms and conditions asserted +by the copyright holder. Transmission or reproduction of protected +items beyond that allowed by fair use (PDF) as defined in the copyright +laws requires the written permission of the copyright owners. NLM +provides no legal advice concerning distribution of copyrighted +materials. Please consult your legal counsel. If you wish to do a large +data mining project on PubMed data, you can enter into a licensing +agreement and lease the data for free from NLM. For more information on +this please see `http://www.nlm.nih.gov/databases/leased.html <http://www.nlm.nih.gov/databases/leased.html>`__ + +The `full disclaimer <http://www.ncbi.nlm.nih.gov/About/disclaimer.html>`__ is available on +their website + +Liability +~~~~~~~~~ + +For documents and software available from this server, the +U.S. Government does not warrant or assume any legal liability or +responsibility for the accuracy, completeness, or usefulness of any +information, apparatus, product, or process disclosed. + +Endorsement +~~~~~~~~~~~ + +NCBI does not endorse or recommend any commercial +products, processes, or services. The views and opinions of authors +expressed on NCBI's Web sites do not necessarily state or reflect those +of the U.S. Government, and they may not be used for advertising or +product endorsement purposes. + +External Links +~~~~~~~~~~~~~~ + +Some NCBI Web pages may provide links to other Internet +sites for the convenience of users. NCBI is not responsible for the +availability or content of these external sites, nor does NCBI endorse, +warrant, or guarantee the products, services, or information described +or offered at these other Internet sites. Users cannot assume that the +external sites will abide by the same Privacy Policy to which NCBI +adheres. It is the responsibility of the user to examine the copyright +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": + --history_file $query_source.history_file +#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 +#end if + </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> + <when value="history"> + <param label="History File" name="history_file" type="data" format="json"/> + </when> + <when value="id_file"> + <param label="ID List" name="id_file" type="data" format="text,tabular"/> + </when> + <when value="id_list"> + <param label="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, + author = {Eric Sayers}, + title = {Entrez Programming Utilities Help}, + year = {2010}, + publisher = {National Center for Biotechnology Information, Bethesda, Maryland}, + note = {http://ww.ncbi.nlm.nih.gov/books/NBK25500/} + }</citation> + </citations> + </xml> + <xml name="requirements"> + <requirements> + <requirement type="package" version="2.7">python</requirement> + <requirement type="package" version="1.66">biopython</requirement> + </requirements> + </xml> + <xml name="linkname"> + <param name="linkname" type="select" label="To NCBI Database"> + <!-- TODO: http://eutils.ncbi.nlm.nih.gov/entrez/query/static/entrezlinks.html --> + </param> + </xml> +</macros>