Mercurial > repos > iuc > beacon2_datasets

comparison datasets.xml @ 0:a38d4a52dbff draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
author iuc
date Mon, 22 Jul 2024 12:36:52 +0000
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children 1f9f549aa9ca
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-1:000000000000 0:a38d4a52dbff
1 <tool id="beacon2_datasets" name="Beacon2 Datasets" version="1.0.0" profile="21.05">
2 <description>Query the datasets collection in the beacon database groupings of variants or individuals who belong to the same repository</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="creators"/>
7 <expand macro="requirements"/>
8 <command detect_errors="exit_code">
9 <![CDATA[
10 beacon2-search datasets
11 --db-host '$db_host'
12 --db-port $db_port
13 --database '$database'
14 --collection '$collection'
15 --advance-connection
16 --db-auth-config '$credentials'
17 #if str($advanced_settings.dataUseConditions)
18 --dataUseConditions '$advanced_settings.dataUseConditions'
19 #end if
20 #if str($advanced_settings.ontologyModifiers)
21 --ontologyModifiers '$advanced_settings.ontologyModifiers'
22 #end if
23 #if str($advanced_settings.identification)
24 --identification '$advanced_settings.identification'
25 #end if
26 #if str($advanced_settings.name)
27 --name '$advanced_settings.name'
28 #end if
29 > datasets_query_findings.json
30 ]]>
31 </command>
32 <expand macro="configfile"/>
33 <inputs>
34 <expand macro="Connection_to_MongoDB"/>
35 <expand macro="Database_Configuration"/>
36 <section name="advanced_settings" title="Advanced settings" expanded="false">
37 <param argument="--dataUseConditions" optional="true" type="text" label="DATAUSECONDITIONS" value="" help="Data use conditions applying to this dataset, e.g. disease specific research" />
38 <param argument="--ontologyModifiers" optional="true" type="text" label="DATA USE CONDITIONS MODIFIERS" value="" help="Modifiers that further specify the datasets, e.g. coronary artery disease" />
39 <param argument="--identification" optional="true" type="text" label="ID" value="" help="Unique identifier of the dataset" />
40 <param argument="--name" optional="true" type="text" label="NAME" value="" help="Name of the dataset" />
41 </section>
42 </inputs>
43 <outputs>
44 <data name="out_datasets_query" format="json" label="${tool.name} on ${on_string}: Datasets Query" from_work_dir="datasets_query_findings.json" />
45 </outputs>
46 <tests>
47 <test expect_num_outputs="1">
48 <param name="database" value="beacon" />
49 <param name="collection" value="datasets" />
50 <param name="db_host" value="20.108.51.167" />
51 <param name="identification" value="refvar-668fcf57aee552bc911b966e" />
52 <param name="name" value="The Genome in a Bottle Consortium (GIAB)" />
53 <output name="out_datasets_query">
54 <assert_contents>
55 <has_text_matching expression="_id"/>
56 </assert_contents>
57 </output>
58 </test>
59 </tests>
60 <help><![CDATA[
61 Beacon2 Datasets queries the datasets collection in the Beacon database to study the variants or individuals in a populations or groups who belong to the same repository.
62 ]]></help>
63 <expand macro="citations" />
64 </tool>