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comparison individuals.xml @ 0:b648eb72552c 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 12:35:16 +0000
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children 72d8cb0fa73f
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-1:000000000000 0:b648eb72552c
1 <tool id="beacon2_individuals" name="Beacon2 Individuals" version="1.0.0" profile="21.05">
2 <description>Query the individuals collection in the beacon database</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 individuals
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($advanced_settings.ageGroup)
18 --ageGroup '$advanced_settings.ageGroup'
19 #end if
20 #if str($advanced_settings.diseaseCode)
21 --diseaseCode '$advanced_settings.diseaseCode'
22 #end if
23 #if str($advanced_settings.familyHistory) and $advanced_settings.familyHistory != ""
24 --familyHistory '$advanced_settings.familyHistory'
25 #end if
26 #if str($advanced_settings.severity)
27 --severity '$advanced_settings.severity'
28 #end if
29 #if str($advanced_settings.stage)
30 --stage '$advanced_settings.stage'
31 #end if
32 #if str($advanced_settings.ethnicity)
33 --ethnicity '$advanced_settings.ethnicity'
34 #end if
35 #if str($advanced_settings.geographicOrigin)
36 --geographicOrigin '$advanced_settings.geographicOrigin'
37 #end if
38 #if str($advanced_settings.identification)
39 --identification '$advanced_settings.identification'
40 #end if
41 #if str($advanced_settings.assayCode)
42 --assayCode '$advanced_settings.assayCode'
43 #end if
44 #if str($advanced_settings.sex) and $advanced_settings.sex != ""
45 --sex '$advanced_settings.sex'
46 #end if
47 > individuals_query_findings.json
48 ]]>
49 </command>
50 <expand macro="configfile"/>
51 <inputs>
52 <expand macro="Connection_to_MongoDB"/>
53 <expand macro="Database_Configuration"/>
54 <section name="advanced_settings" title="Advanced settings" expanded="false">
55 <param argument="--ageGroup" optional="true" type="text" label="AGE GROUP" value="" help="age af onset, e.g. Adult 18-65 Years Old" />
56 <param argument="--diseaseCode" optional="true" type="text" label="DISEASE CODE" value="" help="Disease code, Spinocerebellar ataxia 1" />
57 <param argument="--familyHistory" optional="true" type="select" label="FAMILY HISTORY" help="">
58 <option value="true">true</option>
59 <option value="false">false</option>
60 <option value="" selected="True">unknown</option>
61 </param>
62 <param argument="--severity" optional="true" type="text" label="SEVERITY" value="" help="e.g. Profound" />
63 <param argument="--stage" optional="true" type="text" label="STAGE" value="" help="e.g. acute onset" />
64 <param argument="--ethnicity" optional="true" type="text" label="ETHNICITY" value="" help="e.g. European" />
65 <param argument="--geographicOrigin" optional="true" type="text" label="GEOGRAPHIC ORIGIN" value="" help="e.g. Slovenia" />
66 <param argument="--identification" optional="true" type="text" label="ID" value="" help="Individual identifier (internal ID)" />
67 <param argument="--assayCode" optional="true" type="text" label="ASSAY CODE" value="" help="e.g. Platelets [#/volume] in Blood" />
68 <param argument="--sex" optional="true" type="select" label="SEX" help="">
69 <option value="male">male</option>
70 <option value="female">female</option>
71 <option value="" selected="True">non specific</option>
72 </param>
73 </section>
74 </inputs>
75 <outputs>
76 <data name="out_individuals_query" format="json" label="${tool.name} on ${on_string}: Individuals Query" from_work_dir="individuals_query_findings.json" />
77 </outputs>
78 <tests>
79 <test expect_num_outputs="1">
80 <param name="database" value="beacon" />
81 <param name="collection" value="individuals" />
82 <param name="db_host" value="20.108.51.167" />
83 <param name="sex" value="male" />
84 <param name="geographicOrigin" value="United States of America" />
85 <param name="diseaseCode" value="intolerance" />
86 <param name="ethnicity" value="Han Chinese" />
87 <output name="out_individuals_query">
88 <assert_contents>
89 <has_text_matching expression="_id"/>
90 </assert_contents>
91 </output>
92 </test>
93 </tests>
94 <help><![CDATA[
95 Beacon2 Individuals queries the individuals collection in the Beacon database for either patients or healthy controls whose details (including phenotypic and clinical) are stored in the repository.
96 ]]></help>
97 <expand macro="citations" />
98 </tool>