Mercurial > repos > iuc > ncbi_entrez_direct_esearch

annotate macros.xml @ 3:d75bed16aee8 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit fcd9b48e8c6f5d44bd6e35e2ec6ccad38965e675
author iuc
date Fri, 14 Jun 2024 21:16:20 +0000
parents f6046ed1f915
children 95b5c34650b6
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b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
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1 <macros>
3
d75bed16aee8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit fcd9b48e8c6f5d44bd6e35e2ec6ccad38965e675
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2 <token name="@TOOL_VERSION@">22.1</token>
0
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
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3 <xml name="requirements">
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
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4 <requirements>
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
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5 <requirement type="package" version="@TOOL_VERSION@">entrez-direct</requirement>
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
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6 </requirements>
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
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7 </xml>
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
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8 <token name="@ECONTACT@"><![CDATA[
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
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9 #set $__contact_email__ = ';'.join( str( $__admin_users__ ).split( ',' ) )
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
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10 #if str( $__user_email__ ):
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
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11 #set $__contact_email__ = $__contact_email__ + ";" + str( $__user_email__ )
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
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12 #end if
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
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13 econtact -email "${ __contact_email__ }" -tool "galaxy_ncbi_entrez_direct" > /dev/null ;
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
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14 ]]>
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
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15 </token>
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
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16 <token name="@DISCLAIMER@"><![CDATA[
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
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17 Usage Guidelines and Requirements
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
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18 =================================
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19
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20 Frequency, Timing, and Registration of E-utility URL Requests
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
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21 -------------------------------------------------------------
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22
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
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23 In order not to overload the E-utility servers, NCBI recommends that users
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
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24 limit large jobs to either weekends or between 9:00 PM and 5:00 AM Eastern time
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25 during weekdays. Failure to comply with this policy may result in an IP address
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
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26 being blocked from accessing NCBI.
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27
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28 Minimizing the Number of Requests
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29 ---------------------------------
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30
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31 If a task requires searching for and/or downloading a large number of
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
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32 records, it is much more efficient to use the Entrez History to upload
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
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33 and/or retrieve these records in batches rather than using separate
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34 requests for each record. Please refer to Application 3 in Chapter 3
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
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35 for an example. Many thousands of IDs can be uploaded using a single
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
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36 EPost request, and several hundred records can be downloaded using one
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
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37 EFetch request.
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38
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39
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40 Disclaimer and Copyright Issues
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
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41 -------------------------------
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
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42
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
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43 In accordance with requirements of NCBI's E-Utilities, we must provide
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
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44 the following disclaimer:
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
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45
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
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46 Please note that abstracts in PubMed may incorporate material that may
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
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47 be protected by U.S. and foreign copyright laws. All persons
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
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48 reproducing, redistributing, or making commercial use of this
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49 information are expected to adhere to the terms and conditions asserted
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50 by the copyright holder. Transmission or reproduction of protected
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51 items beyond that allowed by fair use (PDF) as defined in the copyright
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
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52 laws requires the written permission of the copyright owners. NLM
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53 provides no legal advice concerning distribution of copyrighted
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54 materials. Please consult your legal counsel. If you wish to do a large
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
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55 data mining project on PubMed data, you can enter into a licensing
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
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56 agreement and lease the data for free from NLM. For more information on
b6ffd64c448e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 8f96f378620bb663dcce2845ecb14355413f7afa"
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57
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58 The `full disclaimer <https://www.ncbi.nlm.nih.gov/home/about/policies/>`__ is available on
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59 their website
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60
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61 Liability
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62 ~~~~~~~~~
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63
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64 For documents and software available from this server, the
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65 U.S. Government does not warrant or assume any legal liability or
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66 responsibility for the accuracy, completeness, or usefulness of any
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67 information, apparatus, product, or process disclosed.
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68
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69 Endorsement
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70 ~~~~~~~~~~~
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71
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72 NCBI does not endorse or recommend any commercial
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73 products, processes, or services. The views and opinions of authors
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74 expressed on NCBI's Web sites do not necessarily state or reflect those
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75 of the U.S. Government, and they may not be used for advertising or
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76 product endorsement purposes.
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77
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78 External Links
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79 ~~~~~~~~~~~~~~
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80
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81 Some NCBI Web pages may provide links to other Internet
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82 sites for the convenience of users. NCBI is not responsible for the
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83 availability or content of these external sites, nor does NCBI endorse,
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84 warrant, or guarantee the products, services, or information described
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85 or offered at these other Internet sites. Users cannot assume that the
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86 external sites will abide by the same Privacy Policy to which NCBI
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87 adheres. It is the responsibility of the user to examine the copyright
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88 and licensing restrictions of linked pages and to secure all necessary
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89 permissions.
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90 ]]></token>
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91 <xml name="citations">
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92 <citations>
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93 <citation type="bibtex">@Book{ncbiEDirect,
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94 author = {Jonathan Kans},
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95 title = {Entrez Direct: E-utilities on the UNIX Command Line},
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96 year = {2013},
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97 publisher = {National Center for Biotechnology Information, Bethesda, Maryland},
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98 note = {http://www.ncbi.nlm.nih.gov/books/NBK179288/}
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99 }</citation>
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100 </citations>
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101 </xml>
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102 </macros>