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comparison bracket.xml @ 0:bf505cdea06a 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 12:33:21 +0000
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children e8d16ba0bfd6
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-1:000000000000 0:bf505cdea06a
1 <tool id="beacon2_bracket" name="Beacon2 Bracket" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
2 <description>Specifies a sequence ranges for both the start and end positions of a genomic variation</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="creators"/>
7 <expand macro="requirements"/>
8 <command detect_errors="exit_code"><![CDATA[
9 beacon2-search bracket
10 --db-host '$db_host'
11 --db-port $db_port
12 --database '$database'
13 --collection '$collection'
14 --advance-connection
15 --db-auth-config '$credentials'
16 --start-minimum $start_minimum
17 --start-maximum $start_maximum
18 --end-minimum $end_minimum
19 --end-maximum $end_maximum
20 #if str($advanced_settings.variantType)
21 --variantType '$advanced_settings.variantType'
22 #end if
23 #if str($advanced_settings.referenceName)
24 --referenceName '$advanced_settings.referenceName'
25 #end if
26 > bracket_query_findings.json
27 ]]></command>
28 <expand macro="configfile"/>
29 <inputs>
30 <expand macro="Connection_to_MongoDB" />
31 <expand macro="Database_Configuration" />
32 <param argument="--start-minimum" type="integer" label="Start minimum position" value="" help="" />
33 <param argument="--start-maximum" type="integer" label="Start maximum position" value="" help="" />
34 <param argument="--end-minimum" type="integer" label="End minimum position" value="" help="" />
35 <param argument="--end-maximum" type="integer" label="End maximum position" value="" help="" />
36 <section name="advanced_settings" title="Advanced settings" expanded="false">
37 <param argument="--referenceName" optional="true" type="text" label="Reference Name" value="" help="Reference name in numbers chr1/1, chr2/2, chr3/3, etc." />
38 <param argument="--variantType" optional="true" type="text" label="VARIANT TYPE" value="" help="Targeted Variant type to search for" />
39 </section>
40 </inputs>
41 <outputs>
42 <data name="out_bracket_query" format="json" label="${tool.name} on ${on_string}: Bracket Query" from_work_dir="bracket_query_findings.json" />
43 </outputs>
44 <tests>
45 <test expect_num_outputs="1">
46 <param name="database" value="beacon" />
47 <param name="collection" value="genomicVariations" />
48 <param name="db_host" value="20.108.51.167" />
49 <param name="start_minimum" value="131836" />
50 <param name="start_maximum" value="161836" />
51 <param name="end_minimum" value="131837" />
52 <param name="end_maximum" value="151837" />
53 <param name="variantType" value="SNP" />
54 <output name="out_bracket_query">
55 <assert_contents><has_text_matching expression="_id"/></assert_contents>
56 </output>
57 </test>
58 </tests>
59 <help><![CDATA[
60 Bracket Queries allow the specification of sequence ranges for both start and end positions of a genomic variation. The typical example here is the query for similar structural variants - particularly CNVs - affecting a genomic region but potentially differing in their exact base extents.
61 ]]></help>
62 <expand macro="citations" />
63 </tool>