Mercurial > repos > iuc > ncbi_eutils_epost
comparison epost.xml @ 3:ae3a5d753d42 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
author | iuc |
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date | Wed, 23 Sep 2020 09:51:06 +0000 |
parents | 7d868844e952 |
children |
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2:7d868844e952 | 3:ae3a5d753d42 |
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4 <macros> | 4 <macros> |
5 <import>macros.xml</import> | 5 <import>macros.xml</import> |
6 </macros> | 6 </macros> |
7 <expand macro="requirements"/> | 7 <expand macro="requirements"/> |
8 <version_command>python epost.py --version</version_command> | 8 <version_command>python epost.py --version</version_command> |
9 <command detect_errors="aggressive"><![CDATA[ | 9 <command detect_errors="aggressive"> |
10 python '$__tool_directory__/epost.py' | 10 <![CDATA[ |
11 $db_select | |
12 | 11 |
13 @EMAIL_ARGUMENTS@ | 12 python '$__tool_directory__/epost.py' |
14 | 13 |
15 @LIST_OR_HIST@ | 14 $db_select |
16 | 15 |
17 > $history | 16 @EMAIL_ARGUMENTS@ |
18 ]]></command> | 17 |
18 #if $query_source.qss == "id_file": | |
19 --id_list $query_source.id_file | |
20 #else if $query_source.qss == "id_list": | |
21 --id $query_source.id_list | |
22 #else if $query_source.qss == "id_xml": | |
23 --id_xml $query_source.id_xml | |
24 #else if $query_source.qss == "id_json": | |
25 --id_json $query_source.id_json | |
26 #end if | |
27 | |
28 #if $update_history.history_type == "select" and $update_history.history_entry.history_select == "history_json": | |
29 --history_file "$update_history.history_entry.history_file" | |
30 #else if $update_history.history_type == "select" and $update_history.history_entry.history_select == "history_xml": | |
31 --history_xml "$update_history.history_entry.history_xml" | |
32 #else if $update_history.history_type == "paste": | |
33 --webenv "$update_history.webenv" | |
34 #end if | |
35 | |
36 > $history | |
37 | |
38 ]]> | |
39 </command> | |
19 <inputs> | 40 <inputs> |
41 <conditional name="query_source"> | |
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."> | |
43 <option value="id_file" selected="True">ID file (Tabular)</option> | |
44 <option value="id_xml">ID File (XML)</option> | |
45 <option value="id_json">ID File (JSON)</option> | |
46 <option value="id_list">Paste IDs</option> | |
47 </param> | |
48 <when value="id_file"> | |
49 <param label="ID File (Text)" name="id_file" type="data" format="text,tabular" help="A Text file containing one ID per line"/> | |
50 </when> | |
51 <when value="id_xml"> | |
52 <param label="ID File (XML)" name="id_xml" type="data" format="xml" help="ESearch or ELink Result XML file"/> | |
53 </when> | |
54 <when value="id_json"> | |
55 <param label="ID File (JSON)" name="id_json" type="data" format="json" help="ESearch or ELink Result JSON file"/> | |
56 </when> | |
57 <when value="id_list"> | |
58 <param label="Paste ID List" name="id_list" type="text" area="true" help="Newline/Comma separated list of IDs"/> | |
59 </when> | |
60 </conditional> | |
61 | |
20 <expand macro="dbselect"/> | 62 <expand macro="dbselect"/> |
21 <expand macro="list_or_hist"/> | 63 |
64 <conditional name="update_history"> | |
65 <param name="history_type" type="select" label="Target History" help="IDs will be saved to a supplied or created history."> | |
66 <option value="create" selected="True">Create a new history</option> | |
67 <option value="select">Add to an existing history by file</option> | |
68 <option value="paste">Add to an existing history by history (WebEnv) ID</option> | |
69 </param> | |
70 <when value="create"/> | |
71 <when value="select"> | |
72 <conditional name="history_entry"> | |
73 <param name="history_select" type="select" label="Select an existing history"> | |
74 <option value="history_json">History File (JSON)</option> | |
75 <option value="history_xml">History File (XML)</option> | |
76 </param> | |
77 <when value="history_json"> | |
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"/> | |
79 </when> | |
80 <when value="history_xml"> | |
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"/> | |
82 </when> | |
83 </conditional> | |
84 </when> | |
85 <when value="paste"> | |
86 <param name="webenv" type="text" label="WebEnv History ID"/> | |
87 </when> | |
88 </conditional> | |
22 </inputs> | 89 </inputs> |
23 <outputs> | 90 <outputs> |
24 <expand macro="history_out"/> | 91 <data format="json" name="history" label="NCBI History"/> |
25 </outputs> | 92 </outputs> |
26 <tests> | 93 <tests> |
27 <test> | 94 <test> |
28 <param name="db_select" value="nuccore"/> | 95 <param name="db_select" value="nuccore"/> |
29 <param name="qss" value="id_list"/> | 96 <param name="qss" value="id_list"/> |
30 <param name="id_list" value="126697566"/> | 97 <param name="id_list" value="126697566"/> |
31 <output name="history" file="example.history.json" compare="sim_size" delta="10" ftype="json"/> | 98 <param name="history_type" value="create"/> |
99 <output name="history" file="example.history.json" compare="sim_size" delta="70" ftype="json"/> | |
32 </test> | 100 </test> |
33 </tests> | 101 </tests> |
34 <help><![CDATA[ | 102 <help><![CDATA[ |
35 NCBI Entrez EPost | 103 NCBI Entrez EPost |
36 ================= | 104 ================= |