Mercurial > repos > iuc > ncbi_eutils_epost

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 851b88d92fa7740880a5edf407f629bf3f7f7bf0
author iuc
date Fri, 04 Oct 2024 14:34:26 +0000
parents acb271106065
children
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a640698e77d9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit db33413a06c275efd4cc8e771c37facf543a2cfa"
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1 <tool id="ncbi_eutils_epost" name="NCBI EPost" version="@WRAPPER_VERSION@" profile="@PROFILE@">
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2 <description>post UIDs to NCBI History Server</description>
6defb4c34d01 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
6defb4c34d01 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
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6 <expand macro="requirements"/>
6defb4c34d01 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
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7 <version_command>python epost.py --version</version_command>
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8 <command detect_errors="aggressive">
acb271106065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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9 <![CDATA[
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acb271106065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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11 python '$__tool_directory__/epost.py'
acb271106065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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acb271106065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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13 $db_select
acb271106065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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acb271106065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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15 @EMAIL_ARGUMENTS@
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17 #if $query_source.qss == "id_file":
acb271106065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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18 --id_list $query_source.id_file
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19 #else if $query_source.qss == "id_list":
acb271106065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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20 --id $query_source.id_list
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21 #else if $query_source.qss == "id_xml":
acb271106065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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22 --id_xml $query_source.id_xml
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23 #else if $query_source.qss == "id_json":
acb271106065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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24 --id_json $query_source.id_json
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25 #end if
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acb271106065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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27 #if $update_history.history_type == "select" and $update_history.history_entry.history_select == "history_json":
acb271106065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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28 --history_file "$update_history.history_entry.history_file"
acb271106065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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29 #else if $update_history.history_type == "select" and $update_history.history_entry.history_select == "history_xml":
acb271106065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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30 --history_xml "$update_history.history_entry.history_xml"
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31 #else if $update_history.history_type == "paste":
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32 --webenv "$update_history.webenv"
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33 #end if
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acb271106065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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35 > $history
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36
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37 ]]>
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38 </command>
acb271106065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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39 <inputs>
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40 <conditional name="query_source">
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41 <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.">
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42 <option value="id_file" selected="True">ID file (Tabular)</option>
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43 <option value="id_xml">ID File (XML)</option>
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44 <option value="id_json">ID File (JSON)</option>
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45 <option value="id_list">Paste IDs</option>
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46 </param>
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47 <when value="id_file">
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48 <param label="ID File (Text)" name="id_file" type="data" format="text,tabular" help="A Text file containing one ID per line"/>
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49 </when>
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50 <when value="id_xml">
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51 <param label="ID File (XML)" name="id_xml" type="data" format="xml" help="ESearch or ELink Result XML file"/>
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52 </when>
acb271106065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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53 <when value="id_json">
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54 <param label="ID File (JSON)" name="id_json" type="data" format="json" help="ESearch or ELink Result JSON file"/>
acb271106065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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55 </when>
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56 <when value="id_list">
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57 <param label="Paste ID List" name="id_list" type="text" area="true" help="Newline/Comma separated list of IDs"/>
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58 </when>
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59 </conditional>
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60
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61 <expand macro="dbselect"/>
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62
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63 <conditional name="update_history">
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64 <param name="history_type" type="select" label="Target History" help="IDs will be saved to a supplied or created history.">
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65 <option value="create" selected="True">Create a new history</option>
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66 <option value="select">Add to an existing history by file</option>
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67 <option value="paste">Add to an existing history by history (WebEnv) ID</option>
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68 </param>
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69 <when value="create"/>
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70 <when value="select">
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71 <conditional name="history_entry">
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72 <param name="history_select" type="select" label="Select an existing history">
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73 <option value="history_json">History File (JSON)</option>
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74 <option value="history_xml">History File (XML)</option>
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75 </param>
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76 <when value="history_json">
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77 <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"/>
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78 </when>
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79 <when value="history_xml">
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80 <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"/>
acb271106065 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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81 </when>
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82 </conditional>
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83 </when>
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84 <when value="paste">
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85 <param name="webenv" type="text" label="WebEnv History ID"/>
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86 </when>
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87 </conditional>
0
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88 </inputs>
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89 <outputs>
8
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90 <data format="json" name="history" label="NCBI History"/>
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91 </outputs>
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92 <tests>
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93 <test>
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94 <param name="db_select" value="nuccore"/>
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95 <param name="qss" value="id_list"/>
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96 <param name="id_list" value="126697566"/>
8
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97 <param name="history_type" value="create"/>
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98 <output name="history" file="example.history.json" compare="sim_size" delta="70" ftype="json"/>
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99 </test>
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100 </tests>
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101 <help><![CDATA[
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102 NCBI Entrez EPost
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103 =================
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104
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105 Accepts a list of UIDs from a given database, stores the set on the History
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106 Server, and responds with an NCBI History reference.
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107
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108 @REFERENCES@
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109
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110 @DISCLAIMER@
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111 ]]></help>
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112 <expand macro="citations"/>
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113 </tool>