Mercurial > repos > iuc > ncbi_eutils_epost

annotate epost.xml @ 3:ae3a5d753d42 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
author iuc
date Wed, 23 Sep 2020 09:51:06 +0000
parents 7d868844e952
children a64d1a16f04b
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18e6b25259ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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1 <?xml version="1.0"?>
2
7d868844e952 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit db33413a06c275efd4cc8e771c37facf543a2cfa"
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2 <tool id="ncbi_eutils_epost" name="NCBI EPost" version="@WRAPPER_VERSION@" profile="@PROFILE@">
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18e6b25259ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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3 <description>post UIDs to NCBI History Server</description>
18e6b25259ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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4 <macros>
18e6b25259ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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5 <import>macros.xml</import>
18e6b25259ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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6 </macros>
18e6b25259ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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7 <expand macro="requirements"/>
18e6b25259ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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8 <version_command>python epost.py --version</version_command>
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ae3a5d753d42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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9 <command detect_errors="aggressive">
ae3a5d753d42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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10 <![CDATA[
ae3a5d753d42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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ae3a5d753d42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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12 python '$__tool_directory__/epost.py'
ae3a5d753d42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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ae3a5d753d42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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14 $db_select
ae3a5d753d42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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ae3a5d753d42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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16 @EMAIL_ARGUMENTS@
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3
ae3a5d753d42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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18 #if $query_source.qss == "id_file":
ae3a5d753d42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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19 --id_list $query_source.id_file
ae3a5d753d42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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20 #else if $query_source.qss == "id_list":
ae3a5d753d42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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21 --id $query_source.id_list
ae3a5d753d42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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22 #else if $query_source.qss == "id_xml":
ae3a5d753d42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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23 --id_xml $query_source.id_xml
ae3a5d753d42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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24 #else if $query_source.qss == "id_json":
ae3a5d753d42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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25 --id_json $query_source.id_json
ae3a5d753d42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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26 #end if
ae3a5d753d42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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ae3a5d753d42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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28 #if $update_history.history_type == "select" and $update_history.history_entry.history_select == "history_json":
ae3a5d753d42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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29 --history_file "$update_history.history_entry.history_file"
ae3a5d753d42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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30 #else if $update_history.history_type == "select" and $update_history.history_entry.history_select == "history_xml":
ae3a5d753d42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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31 --history_xml "$update_history.history_entry.history_xml"
ae3a5d753d42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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32 #else if $update_history.history_type == "paste":
ae3a5d753d42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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33 --webenv "$update_history.webenv"
ae3a5d753d42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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34 #end if
ae3a5d753d42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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ae3a5d753d42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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36 > $history
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37
3
ae3a5d753d42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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38 ]]>
ae3a5d753d42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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39 </command>
ae3a5d753d42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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40 <inputs>
ae3a5d753d42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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41 <conditional name="query_source">
ae3a5d753d42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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42 <param name="qss" type="select" label="Enter Query IDs by..." help="Files output by ELink or ESearch are acceptable. Query IDs in an ELink result are ignored.">
ae3a5d753d42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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43 <option value="id_file" selected="True">ID file (Tabular)</option>
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44 <option value="id_xml">ID File (XML)</option>
ae3a5d753d42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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45 <option value="id_json">ID File (JSON)</option>
ae3a5d753d42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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46 <option value="id_list">Paste IDs</option>
ae3a5d753d42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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47 </param>
ae3a5d753d42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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48 <when value="id_file">
ae3a5d753d42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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49 <param label="ID File (Text)" name="id_file" type="data" format="text,tabular" help="A Text file containing one ID per line"/>
ae3a5d753d42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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50 </when>
ae3a5d753d42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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51 <when value="id_xml">
ae3a5d753d42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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52 <param label="ID File (XML)" name="id_xml" type="data" format="xml" help="ESearch or ELink Result XML file"/>
ae3a5d753d42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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53 </when>
ae3a5d753d42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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54 <when value="id_json">
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55 <param label="ID File (JSON)" name="id_json" type="data" format="json" help="ESearch or ELink Result JSON file"/>
ae3a5d753d42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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56 </when>
ae3a5d753d42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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57 <when value="id_list">
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58 <param label="Paste ID List" name="id_list" type="text" area="true" help="Newline/Comma separated list of IDs"/>
ae3a5d753d42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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59 </when>
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60 </conditional>
ae3a5d753d42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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61
ae3a5d753d42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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62 <expand macro="dbselect"/>
0
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63
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64 <conditional name="update_history">
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65 <param name="history_type" type="select" label="Target History" help="IDs will be saved to a supplied or created history.">
ae3a5d753d42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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66 <option value="create" selected="True">Create a new history</option>
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67 <option value="select">Add to an existing history by file</option>
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68 <option value="paste">Add to an existing history by history (WebEnv) ID</option>
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69 </param>
ae3a5d753d42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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70 <when value="create"/>
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71 <when value="select">
ae3a5d753d42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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72 <conditional name="history_entry">
ae3a5d753d42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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73 <param name="history_select" type="select" label="Select an existing history">
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74 <option value="history_json">History File (JSON)</option>
ae3a5d753d42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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75 <option value="history_xml">History File (XML)</option>
ae3a5d753d42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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76 </param>
ae3a5d753d42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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77 <when value="history_json">
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78 <param label="History File (JSON)" name="history_file" type="data" format="json" help="A JSON file containing the WebEnv ID referencing the history on the NCBI history server to which to add the IDs"/>
ae3a5d753d42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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79 </when>
ae3a5d753d42 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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80 <when value="history_xml">
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81 <param label="History File (XML)" name="history_xml" type="data" format="xml" help="An XML file containing the WebEnv ID referencing the history on the NCBI history server to which to add the IDs"/>
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82 </when>
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83 </conditional>
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84 </when>
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85 <when value="paste">
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86 <param name="webenv" type="text" label="WebEnv History ID"/>
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87 </when>
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88 </conditional>
0
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89 </inputs>
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90 <outputs>
3
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91 <data format="json" name="history" label="NCBI History"/>
0
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92 </outputs>
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93 <tests>
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94 <test>
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95 <param name="db_select" value="nuccore"/>
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96 <param name="qss" value="id_list"/>
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97 <param name="id_list" value="126697566"/>
3
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98 <param name="history_type" value="create"/>
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99 <output name="history" file="example.history.json" compare="sim_size" delta="70" ftype="json"/>
0
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100 </test>
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101 </tests>
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102 <help><![CDATA[
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103 NCBI Entrez EPost
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104 =================
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105
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106 Accepts a list of UIDs from a given database, stores the set on the History
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107 Server, and responds with an NCBI History reference.
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108
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109 @REFERENCES@
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110
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111 @DISCLAIMER@
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112 ]]></help>
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113 <expand macro="citations"/>
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114 </tool>