Mercurial > repos > iuc > ncbi_eutils_esummary

comparison esummary.xml @ 3:254f40d3ae2b 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 09:50:11 +0000
parents cb5a0fe9e036
children
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2:cb5a0fe9e036 3:254f40d3ae2b
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 esummary.py --version</version_command> 8 <version_command>python esummary.py --version</version_command>
9 <command detect_errors="aggressive"><![CDATA[ 9 <command detect_errors="aggressive">
10 python '$__tool_directory__/esummary.py' 10 <![CDATA[
11 $db_select
12 11
13 @LIST_OR_HIST@ 12 python '$__tool_directory__/esummary.py'
14 13
14 $db_select
15 15
16 @EMAIL_ARGUMENTS@ 16 @LIST_OR_HIST@
17 > $default]]></command> 17
18 @EMAIL_ARGUMENTS@
19
20 #if $retstart is not None:
21 --retstart '$retstart'
22 #end if
23
24 #if $retmax is not None:
25 --retmax '$retmax'
26 #end if
27
28 #if $output_format == 'xml':
29 --retmode xml
30 #elif $output_format == 'json':
31 --retmode json
32 #end if
33
34 > $default
35
36 ]]>
37 </command>
18 <inputs> 38 <inputs>
39 <expand macro="list_or_hist"/>
19 <expand macro="dbselect"/> 40 <expand macro="dbselect"/>
20 <expand macro="list_or_hist"/> 41 <param name="retstart" type="integer" value="0" min="0" max="99999" label="Starting record to return (--retstart)" />
42 <param name="retmax" type="integer" value="100000" min="1" max="100000" label="Maximum number of records to return (--retmax)" />
43 <param name="output_format" type="select" label="Output Format">
44 <option value="xml" selected="True">XML</option>
45 <option value="json">JSON</option>
46 </param>
21 </inputs> 47 </inputs>
22 <outputs> 48 <outputs>
23 <data format="xml" name="default" label="Summary of NCBI Search"/> 49 <data format="xml" name="default" label="Summary of NCBI Search">
50 <change_format>
51 <when input="output_format" value="xml" format="xml" />
52 <when input="output_format" value="json" format="json" />
53 </change_format>
54 <filter>query_source['qss'] != 'history_json' and query_source['qss'] != 'history_xml'</filter>
55 </data>
56 <collection name="summaries" type="list" label="Summary of NCBI Searches">
57 <discover_datasets pattern="__designation_and_ext__" directory="downloads"/>
58 <filter>query_source['qss'] == 'history_json' or query_source['qss'] == 'history_xml'</filter>
59 </collection>
24 </outputs> 60 </outputs>
25 <tests> 61 <tests>
26 <test> 62 <test>
27 <param name="qss" value="id_list"/> 63 <param name="qss" value="id_list"/>
28 <param name="id_list" value="10239"/> 64 <param name="id_list" value="10239"/>
29 <param name="db_select" value="taxonomy"/> 65 <param name="db_select" value="taxonomy"/>
66 <param name="retstart" value="0"/>
67 <param name="retmax" value="100000"/>
68 <param name="output_format" value="xml"/>
30 <output name="default" file="esummary.tax.xml" ftype="xml"/> 69 <output name="default" file="esummary.tax.xml" ftype="xml"/>
31 </test> 70 </test>
32 </tests> 71 </tests>
33 <help><![CDATA[ 72 <help><![CDATA[
34 NCBI Entrez ESummary 73 NCBI Entrez ESummary