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comparison range.xml @ 0:36cd015a8eea 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 12:34:31 +0000
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children 6b2ef850f7af
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-1:000000000000 0:36cd015a8eea
1 <tool id="beacon2_range" name="Beacon2 Range" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
2 <description>Retrieve the genomic variants from the beacon database by specifying start and end positions</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 range
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 $start
17 --end $end
18 #if str($advanced_settings.referenceName)
19 --referenceName '$advanced_settings.referenceName'
20 #end if
21 #if str($advanced_settings.alternateBases)
22 --alternateBases '$advanced_settings.alternateBases'
23 #end if
24 #if str($advanced_settings.variantType)
25 --variantType '$advanced_settings.variantType'
26 #end if
27 #if str($advanced_settings.aminoacidChange)
28 --aminoacidChange '$advanced_settings.aminoacidChange'
29 #end if
30 #if str($advanced_settings.variantMinLength)
31 --variantMinLength $advanced_settings.variantMinLength
32 #end if
33 #if str($advanced_settings.variantMaxLength)
34 --variantMaxLength $advanced_settings.variantMaxLength
35 #end if
36 > ranged_query_findings.json
37 ]]></command>
38 <expand macro="configfile"/>
39 <inputs>
40 <expand macro="Connection_to_MongoDB" />
41 <expand macro="Database_Configuration" />
42 <param argument="--start" type="integer" label="START" value="" help="Start position" />
43 <param argument="--end" type="integer" label="END" value="" help="End position" />
44 <section name="advanced_settings" title="Advanced settings" expanded="false">
45 <param argument="--referenceName" optional="true" type="text" label="REFERENCENAME" value="" help="Reference name in numbers chr1/1, chr2/2, chr3/3, etc." />
46 <param argument="--alternateBases" optional="true" type="text" label="ALTERNATEBASES" value="" help="Targeted Alternate bases to search for" />
47 <param argument="--variantType" optional="true" type="text" label="VARIANT TYPE" value="" help="Targeted Variant type to search for" />
48 <param argument="--aminoacidChange" optional="true" type="text" label="AMINOACID CHANGE" value="" help="Targeted Amino acid change to search for" />
49 <param argument="--variantMinLength" optional="true" type="integer" label="VARIANT MIN LENGTH" value="" help="Targeted Variant minimum length to search for" />
50 <param argument="--variantMaxLength" optional="true" type="integer" label="VARIANT MAX LENGTH" value="" help="Targeted VVariant maximum length to search for" />
51 </section>
52 </inputs>
53 <outputs>
54 <data name="out_ranged_query" format="json" label="${tool.name} on ${on_string}: Range Query" from_work_dir="ranged_query_findings.json" />
55 </outputs>
56 <tests>
57 <test expect_num_outputs="1">
58 <param name="database" value="beacon" />
59 <param name="collection" value="genomicVariations" />
60 <param name="db_host" value="20.108.51.167" />
61 <param name="start" value="131836" />
62 <param name="end" value="131837" />
63 <param name="variantType" value="SNP" />
64 <output name="out_ranged_query">
65 <assert_contents><has_text_matching expression="_id"/></assert_contents>
66 </output>
67 </test>
68 </tests>
69 <help><![CDATA[
70 Beacon Range Queries are supposed to return matches of any variant with at least partial overlap of the sequence range specified by reference_name, start and end parameters
71 ]]></help>
72 <expand macro="citations" />
73 </tool>