Mercurial > repos > iuc > ncbi_eutils_efetch

<?xml version="1.0"?>
<macros>
  <token name="@WRAPPER_VERSION@">1.0</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="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="epigenomics">Epigenomics</option>
      <option value="gap">dbGaP</option>
      <option value="gds">GEO Datasets</option>
      <option value="gene">Gene</option>
      <option value="genome">Genome</option>
      <option value="geoprofiles">GEO Profiles</option>
      <option value="gtr">Genetic Testing Registry</option>
      <option value="homologene">HomoloGene</option>
      <option value="journals">Journals</option>
      <option value="medgen">MedGen</option>
      <option value="mesh">MeSH</option>
      <option value="ncbisearch">NCBI Web Site</option>
      <option value="nlmcatalog">NLM Catalog</option>
      <option value="nuccore">Nucleotide</option>
      <option value="nucest">EST</option>
      <option value="nucgss">GSS</option>
      <option value="omim">OMIM</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="snp">SNP</option>
      <option value="sra">SRA</option>
      <option value="structure">Structure</option>
      <option value="taxonomy">Taxonomy</option>
      <option value="toolkit">NCBI C++ Toolkit</option>
      <option value="toolkitall">NCBI C++ Toolkit All</option>
      <option value="toolkitbook">NCBI C++ Toolkit Book</option>
      <option value="unigene">UniGene</option>
    </param>
  </xml>
  <xml name="db">
    <conditional name="db">
      <expand macro="dbselect" />
      <when value="assembly">
        <param name="output_format" type="select" label="Output Format">
          <option value="docsum-xml">Document summary</option>
          <option value="uilist-xml">List of UIDs (XML)</option>
          <option value="uilist-text">List of UIDs (plain text)</option>
        </param>
      </when>
      <when value="bioproject">
        <param name="output_format" type="select" label="Output Format">
          <option value="docsum-xml">Document summary</option>
          <option value="uilist-xml">List of UIDs (XML)</option>
          <option value="uilist-text">List of UIDs (plain text)</option>
          <option value="xml-xml">Full record</option>
        </param>
      </when>
      <when value="biosample">
        <param name="output_format" type="select" label="Output Format">
          <option value="docsum-xml">Document summary</option>
          <option value="uilist-xml">List of UIDs (XML)</option>
          <option value="uilist-text">List of UIDs (plain text)</option>
          <option value="full-xml">Full record (XML)</option>
          <option value="full-text">Full record (plain text)</option>
        </param>
      </when>
      <when value="biosystems">
        <param name="output_format" type="select" label="Output Format">
          <option value="docsum-xml">Document summary</option>
          <option value="uilist-xml">List of UIDs (XML)</option>
          <option value="uilist-text">List of UIDs (plain text)</option>
          <option value="xml-xml">Full record</option>
        </param>
      </when>
      <when value="blastdbinfo">
        <param name="output_format" type="select" label="Output Format">
          <option value="docsum-xml">Document summary</option>
          <option value="uilist-xml">List of UIDs (XML)</option>
          <option value="uilist-text">List of UIDs (plain text)</option>
        </param>
      </when>
      <when value="books">
        <param name="output_format" type="select" label="Output Format">
          <option value="docsum-xml">Document summary</option>
          <option value="uilist-xml">List of UIDs (XML)</option>
          <option value="uilist-text">List of UIDs (plain text)</option>
        </param>
      </when>
      <when value="cdd">
        <param name="output_format" type="select" label="Output Format">
          <option value="docsum-xml">Document summary</option>
          <option value="uilist-xml">List of UIDs (XML)</option>
          <option value="uilist-text">List of UIDs (plain text)</option>
        </param>
      </when>
      <when value="clinvar">
        <param name="output_format" type="select" label="Output Format">
          <option value="docsum-xml">Document summary</option>
          <option value="uilist-xml">List of UIDs (XML)</option>
          <option value="uilist-text">List of UIDs (plain text)</option>
        </param>
      </when>
      <when value="clone">
        <param name="output_format" type="select" label="Output Format">
          <option value="docsum-xml">Document summary</option>
          <option value="uilist-xml">List of UIDs (XML)</option>
          <option value="uilist-text">List of UIDs (plain text)</option>
        </param>
      </when>
      <when value="dbvar">
        <param name="output_format" type="select" label="Output Format">
          <option value="docsum-xml">Document summary</option>
          <option value="uilist-xml">List of UIDs (XML)</option>
          <option value="uilist-text">List of UIDs (plain text)</option>
        </param>
      </when>
      <when value="epigenomics">
        <param name="output_format" type="select" label="Output Format">
          <option value="docsum-xml">Document summary</option>
          <option value="uilist-xml">List of UIDs (XML)</option>
          <option value="uilist-text">List of UIDs (plain text)</option>
        </param>
      </when>
      <when value="gap">
        <param name="output_format" type="select" label="Output Format">
          <option value="docsum-xml">Document summary</option>
          <option value="uilist-xml">List of UIDs (XML)</option>
          <option value="uilist-text">List of UIDs (plain text)</option>
        </param>
      </when>
      <when value="gds">
        <param name="output_format" type="select" label="Output Format">
          <option value="docsum-xml">Document summary</option>
          <option value="uilist-xml">List of UIDs (XML)</option>
          <option value="uilist-text">List of UIDs (plain text)</option>
          <option value="summary-text">Summary</option>
        </param>
      </when>
      <when value="gene">
        <param name="output_format" type="select" label="Output Format">
          <option value="docsum-xml">Document summary</option>
          <option value="uilist-xml">List of UIDs (XML)</option>
          <option value="uilist-text">List of UIDs (plain text)</option>
          <option value="null-asn.1">text (ASN.1)</option>
          <option value="null-xml">XML</option>
          <option value="gene_table-text">Gene table</option>
        </param>
      </when>
      <when value="genome">
        <param name="output_format" type="select" label="Output Format">
          <option value="docsum-xml">Document summary</option>
          <option value="uilist-xml">List of UIDs (XML)</option>
          <option value="uilist-text">List of UIDs (plain text)</option>
        </param>
      </when>
      <when value="geoprofiles">
        <param name="output_format" type="select" label="Output Format">
          <option value="docsum-xml">Document summary</option>
          <option value="uilist-xml">List of UIDs (XML)</option>
          <option value="uilist-text">List of UIDs (plain text)</option>
        </param>
      </when>
      <when value="gtr">
        <param name="output_format" type="select" label="Output Format">
          <option value="docsum-xml">Document summary</option>
          <option value="uilist-xml">List of UIDs (XML)</option>
          <option value="uilist-text">List of UIDs (plain text)</option>
        </param>
      </when>
      <when value="homologene">
        <param name="output_format" type="select" label="Output Format">
          <option value="docsum-xml">Document summary</option>
          <option value="uilist-xml">List of UIDs (XML)</option>
          <option value="uilist-text">List of UIDs (plain text)</option>
          <option value="null-asn.1">text ASN.1</option>
          <option value="null-xml">XML</option>
          <option value="alignmentscores-text">Alignment scores</option>
          <option value="fasta-text">FASTA</option>
          <option value="homologene-text">HomoloGene</option>
        </param>
      </when>
      <when value="journals">
        <param name="output_format" type="select" label="Output Format">
          <option value="docsum-xml">Document summary</option>
          <option value="uilist-xml">List of UIDs (XML)</option>
          <option value="uilist-text">List of UIDs (plain text)</option>
        </param>
      </when>
      <when value="medgen">
        <param name="output_format" type="select" label="Output Format">
          <option value="docsum-xml">Document summary</option>
          <option value="uilist-xml">List of UIDs (XML)</option>
          <option value="uilist-text">List of UIDs (plain text)</option>
        </param>
      </when>
      <when value="mesh">
        <param name="output_format" type="select" label="Output Format">
          <option value="docsum-xml">Document summary</option>
          <option value="uilist-xml">List of UIDs (XML)</option>
          <option value="uilist-text">List of UIDs (plain text)</option>
          <option value="full-text">Full record</option>
        </param>
      </when>
      <when value="ncbisearch">
        <param name="output_format" type="select" label="Output Format">
          <option value="docsum-xml">Document summary</option>
          <option value="uilist-xml">List of UIDs (XML)</option>
          <option value="uilist-text">List of UIDs (plain text)</option>
        </param>
      </when>
      <when value="nlmcatalog">
        <param name="output_format" type="select" label="Output Format">
          <option value="docsum-xml">Document summary</option>
          <option value="uilist-xml">List of UIDs (XML)</option>
          <option value="uilist-text">List of UIDs (plain text)</option>
          <option value="null-text">Full record</option>
          <option value="null-xml">XML</option>
        </param>
      </when>
      <when value="nuccore">
        <param name="output_format" type="select" label="Output Format">
          <option value="docsum-xml">Document summary</option>
          <option value="uilist-xml">List of UIDs (XML)</option>
          <option value="uilist-text">List of UIDs (plain text)</option>
          <option value="null-text">text ASN.1</option>
          <option value="null-asn.1">binary ASN.1</option>
          <option value="native-xml">Full record in XML</option>
          <option value="acc-text">Accession number(s)</option>
          <option value="fasta-text">FASTA</option>
          <option value="fasta-xml">TinySeq XML</option>
          <option value="seqid-text">SeqID string</option>
          <option value="gb-text">GenBank flat file</option>
          <option value="gb-xml">GBSeq XML</option>
          <option value="gbc-xml">INSDSeq XML</option>
          <option value="ft-text">Feature table</option>
          <option value="gbwithparts-text">GenBank flat file with full sequence (contigs)</option>
          <option value="fasta_cds_na-text">CDS nucleotide FASTA</option>
          <option value="fasta_cds_aa-text">CDS protein FASTA</option>
        </param>
      </when>
      <when value="nucest">
        <param name="output_format" type="select" label="Output Format">
          <option value="docsum-xml">Document summary</option>
          <option value="uilist-xml">List of UIDs (XML)</option>
          <option value="uilist-text">List of UIDs (plain text)</option>
          <option value="null-text">text ASN.1</option>
          <option value="null-asn.1">binary ASN.1</option>
          <option value="native-xml">Full record in XML</option>
          <option value="acc-text">Accession number(s)</option>
          <option value="fasta-text">FASTA</option>
          <option value="fasta-xml">TinySeq XML</option>
          <option value="seqid-text">SeqID string</option>
          <option value="gb-text">GenBank flat file</option>
          <option value="gb-xml">GBSeq XML</option>
          <option value="gbc-xml">INSDSeq XML</option>
          <option value="est-text">EST report</option>
        </param>
      </when>
      <when value="nucgss">
        <param name="output_format" type="select" label="Output Format">
          <option value="docsum-xml">Document summary</option>
          <option value="uilist-xml">List of UIDs (XML)</option>
          <option value="uilist-text">List of UIDs (plain text)</option>
          <option value="null-text">text ASN.1</option>
          <option value="null-asn.1">binary ASN.1</option>
          <option value="native-xml">Full record in XML</option>
          <option value="acc-text">Accession number(s)</option>
          <option value="fasta-text">FASTA</option>
          <option value="fasta-xml">TinySeq XML</option>
          <option value="seqid-text">SeqID string</option>
          <option value="gb-text">GenBank flat file</option>
          <option value="gb-xml">GBSeq XML</option>
          <option value="gbc-xml">INSDSeq XML</option>
          <option value="gss-text">GSS report</option>
        </param>
      </when>
      <when value="omim">
        <param name="output_format" type="select" label="Output Format">
          <option value="docsum-xml">Document summary</option>
          <option value="uilist-xml">List of UIDs (XML)</option>
          <option value="uilist-text">List of UIDs (plain text)</option>
        </param>
      </when>
      <when value="pcassay">
        <param name="output_format" type="select" label="Output Format">
          <option value="docsum-xml">Document summary</option>
          <option value="uilist-xml">List of UIDs (XML)</option>
          <option value="uilist-text">List of UIDs (plain text)</option>
        </param>
      </when>
      <when value="pccompound">
        <param name="output_format" type="select" label="Output Format">
          <option value="docsum-xml">Document summary</option>
          <option value="uilist-xml">List of UIDs (XML)</option>
          <option value="uilist-text">List of UIDs (plain text)</option>
        </param>
      </when>
      <when value="pcsubstance">
        <param name="output_format" type="select" label="Output Format">
          <option value="docsum-xml">Document summary</option>
          <option value="uilist-xml">List of UIDs (XML)</option>
          <option value="uilist-text">List of UIDs (plain text)</option>
        </param>
      </when>
      <when value="pmc">
        <param name="output_format" type="select" label="Output Format">
          <option value="docsum-xml">Document summary</option>
          <option value="uilist-xml">List of UIDs (XML)</option>
          <option value="uilist-text">List of UIDs (plain text)</option>
          <option value="null-xml">XML</option>
          <option value="medline-text">MEDLINE</option>
        </param>
      </when>
      <when value="popset">
        <param name="output_format" type="select" label="Output Format">
          <option value="docsum-xml">Document summary</option>
          <option value="uilist-xml">List of UIDs (XML)</option>
          <option value="uilist-text">List of UIDs (plain text)</option>
          <option value="null-text">text ASN.1</option>
          <option value="null-asn.1">binary ASN.1</option>
          <option value="native-xml">Full record in XML</option>
          <option value="acc-text">Accession number(s)</option>
          <option value="fasta-text">FASTA</option>
          <option value="fasta-xml">TinySeq XML</option>
          <option value="seqid-text">SeqID string</option>
          <option value="gb-text">GenBank flat file</option>
          <option value="gb-xml">GBSeq XML</option>
          <option value="gbc-xml">INSDSeq XML</option>
        </param>
      </when>
      <when value="probe">
        <param name="output_format" type="select" label="Output Format">
          <option value="docsum-xml">Document summary</option>
          <option value="uilist-xml">List of UIDs (XML)</option>
          <option value="uilist-text">List of UIDs (plain text)</option>
        </param>
      </when>
      <when value="protein">
        <param name="output_format" type="select" label="Output Format">
          <option value="docsum-xml">Document summary</option>
          <option value="uilist-xml">List of UIDs (XML)</option>
          <option value="uilist-text">List of UIDs (plain text)</option>
          <option value="null-text">text ASN.1</option>
          <option value="null-asn.1">binary ASN.1</option>
          <option value="native-xml">Full record in XML</option>
          <option value="acc-text">Accession number(s)</option>
          <option value="fasta-text">FASTA</option>
          <option value="fasta-xml">TinySeq XML</option>
          <option value="seqid-text">SeqID string</option>
          <option value="ft-text">Feature table</option>
          <option value="gp-text">GenPept flat file</option>
          <option value="gp-xml">GBSeq XML</option>
          <option value="gpc-xml">INSDSeq XML</option>
          <option value="ipg-xml">Identical Protein XML</option>
        </param>
      </when>
      <when value="proteinclusters">
        <param name="output_format" type="select" label="Output Format">
          <option value="docsum-xml">Document summary</option>
          <option value="uilist-xml">List of UIDs (XML)</option>
          <option value="uilist-text">List of UIDs (plain text)</option>
        </param>
      </when>
      <when value="pubmed">
        <param name="output_format" type="select" label="Output Format">
          <option value="docsum-xml">Document summary</option>
          <option value="uilist-xml">List of UIDs (XML)</option>
          <option value="uilist-text">List of UIDs (plain text)</option>
          <option value="null-asn.1">text ASN.1</option>
          <option value="null-xml">XML</option>
          <option value="medline-text">MEDLINE</option>
          <option value="uilist-text">PMID list</option>
          <option value="abstract-text">Abstract</option>
        </param>
      </when>
      <when value="pubmedhealth">
        <param name="output_format" type="select" label="Output Format">
          <option value="docsum-xml">Document summary</option>
          <option value="uilist-xml">List of UIDs (XML)</option>
          <option value="uilist-text">List of UIDs (plain text)</option>
        </param>
      </when>
      <when value="snp">
        <param name="output_format" type="select" label="Output Format">
          <option value="docsum-xml">Document summary</option>
          <option value="uilist-xml">List of UIDs (XML)</option>
          <option value="uilist-text">List of UIDs (plain text)</option>
          <option value="null-asn.1">text ASN.1</option>
          <option value="null-xml">XML</option>
          <option value="flt-text">Flat file</option>
          <option value="fasta-text">FASTA</option>
          <option value="rsr-text">RS Cluster report</option>
          <option value="ssexemplar-text">SS Exemplar list</option>
          <option value="chr-text">Chromosome report</option>
          <option value="docset-text">Summary</option>
          <option value="uilist-xml">UID list (XML)</option>
          <option value="uilist-text">UID list (text)</option>
        </param>
      </when>
      <when value="sra">
        <param name="output_format" type="select" label="Output Format">
          <option value="docsum-xml">Document summary</option>
          <option value="uilist-xml">List of UIDs (XML)</option>
          <option value="uilist-text">List of UIDs (plain text)</option>
          <option value="full-xml">XML</option>
        </param>
      </when>
      <when value="structure">
        <param name="output_format" type="select" label="Output Format">
          <option value="docsum-xml">Document summary</option>
          <option value="uilist-xml">List of UIDs (XML)</option>
          <option value="uilist-text">List of UIDs (plain text)</option>
        </param>
      </when>
      <when value="taxonomy">
        <param name="output_format" type="select" label="Output Format">
          <option value="docsum-xml">Document summary</option>
          <option value="uilist-xml">List of UIDs (XML)</option>
          <option value="uilist-text">List of UIDs (plain text)</option>
          <option value="null-xml">XML</option>
          <option value="uilist-xml">TaxID list (XML)</option>
          <option value="uilist-text">TaxID list (text)</option>
        </param>
      </when>
    </conditional>
  </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="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>
author	iuc
date	Mon, 02 Nov 2015 12:59:23 -0500
parents	1b4ac594d02a
children	cf56005c4320