annotate macros.xml @ 2:59dfa639e78e draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 1bd7defa5ac7ea1e619c519d719f5bd10452339b

<macros>
    <token name="@TOOL_VERSION@">21.6</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">entrez-direct</requirement>
        </requirements>
    </xml>
    <token name="@ECONTACT@"><![CDATA[
        #set $__contact_email__ = ';'.join( str( $__admin_users__ ).split( ',' ) )
        #if str( $__user_email__ ):
            #set $__contact_email__ = $__contact_email__ + ";" + str( $__user_email__ )
        #end if
        econtact -email "${ __contact_email__ }" -tool "galaxy_ncbi_entrez_direct" > /dev/null ;
        ]]>        
    </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

The `full disclaimer <https://www.ncbi.nlm.nih.gov/home/about/policies/>`__ 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="citations">
        <citations>
            <citation type="bibtex">@Book{ncbiEDirect,
          author = {Jonathan Kans},
          title = {Entrez Direct: E-utilities on the UNIX Command Line},
          year = {2013},
          publisher = {National Center for Biotechnology Information, Bethesda, Maryland},
          note = {http://www.ncbi.nlm.nih.gov/books/NBK179288/}
            }</citation>
        </citations>
    </xml>
</macros>