diff macros.xml @ 0:c66f2400ecf8 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
author iuc
date Tue, 22 Mar 2022 22:30:36 +0000
parents
children c06dcadf986c
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Tue Mar 22 22:30:36 2022 +0000
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+<macros>
+    <token name="@TOOL_VERSION@">13.3</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>