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comparison sequence.xml @ 0:f14c8c011f01 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 12:33:53 +0000
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children 94f3eb8da2b3
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-1:000000000000 0:f14c8c011f01
1 <tool id="beacon2_sequence" name="Beacon2 Sequence" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
2 <description>ŁŽQuery for the existence of a specified sequence at a given genomic position</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 sequence
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 --alternateBases '$alternateBases'
17 --referenceBases '$referenceBases'
18 #if str($advanced_settings.referenceName)
19 --referenceName '$advanced_settings.referenceName'
20 #end if
21 #if str($advanced_settings.start)
22 --start $advanced_settings.start
23 #end if
24 #if str($advanced_settings.collectionIds)
25 --collectionIds '$advanced_settings.collectionIds'
26 #end if
27 > sequenced_query_findings.json
28 ]]></command>
29 <expand macro="configfile"/>
30 <inputs>
31 <expand macro="Connection_to_MongoDB" />
32 <expand macro="Database_Configuration" />
33 <param argument="--alternateBases" type="text" label="Alternate bases" value="" help="" />
34 <param argument="--referenceBases" type="text" label="Reference bases" value="" help="" />
35 <section name="advanced_settings" title="Advanced settings" expanded="false">
36 <param argument="--referenceName" optional="true" type="text" label="REFERENCENAME" value="" help="Reference name in numbers chr1/1, chr2/2, chr3/3, etc." />
37 <param argument="--start" optional="true" type="integer" label="START" value="" help="Start position" />
38 <param argument="--collectionIds" optional="true" type="text" label="Collection ID" value="" help="Datasets ID" />
39 </section>
40 </inputs>
41 <outputs>
42 <data name="out_sequence_query" format="json" label="${tool.name} on ${on_string}: Sequence Query" from_work_dir="sequenced_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" value="10176" />
50 <param name="alternateBases" value="AC" />
51 <param name="referenceBases" value="A" />
52 <output name="out_sequence_query">
53 <assert_contents><has_text_matching expression="_id"/></assert_contents>
54 </output>
55 </test>
56 </tests>
57 <help><![CDATA[
58 Sequence Queries query for the existence of a specified sequence at a given genomic position. Such queries correspond to the original Beacon queries and are used to match short, precisely defined genomic variants such as SNVs and INDELs.
59 ]]></help>
60 <expand macro="citations" />
61 </tool>