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comparison gene.xml @ 0:8e949a739eaa 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 12:36:40 +0000
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children 9135f3e914b7
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-1:000000000000 0:8e949a739eaa
1 <tool id="beacon2_gene" name="Beacon2 Gene" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
2 <description>Queries the beacon database and retrieve the genomic variants matching gene symbol</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 gene
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 --geneId $geneId
17 #if str($advanced_settings.alternateBases)
18 --alternateBases '$advanced_settings.alternateBases'
19 #end if
20 #if str($advanced_settings.variantType)
21 --variantType '$advanced_settings.variantType'
22 #end if
23 #if str($advanced_settings.aminoacidChange)
24 --aminoacidChange '$advanced_settings.aminoacidChange'
25 #end if
26 #if str($advanced_settings.variantMinLength)
27 --variantMinLength $advanced_settings.variantMinLength
28 #end if
29 #if str($advanced_settings.variantMaxLength)
30 --variantMaxLength $advanced_settings.variantMaxLength
31 #end if
32 > gene_query_findings.json
33 ]]></command>
34 <expand macro="configfile"/>
35 <inputs>
36 <expand macro="Connection_to_MongoDB" />
37 <expand macro="Database_Configuration" />
38 <param argument="--geneId" type="text" label="Gene Id" value="" help="" />
39 <section name="advanced_settings" title="Advanced settings" expanded="false">
40 <param argument="--alternateBases" optional="true" type="text" label="ALTERNATEBASES" value="" help="Targeted Alternate bases to search for" />
41 <param argument="--variantType" optional="true" type="text" label="VARIANT TYPE" value="" help="Targeted Variant type to search for" />
42 <param argument="--aminoacidChange" optional="true" type="text" label="AMINOACID CHANGE" value="" help="Targeted Amino acid change to search for" />
43 <param argument="--variantMinLength" optional="true" type="integer" label="VARIANT MIN LENGTH" value="" help="Targeted Variant minimum length to search for" />
44 <param argument="--variantMaxLength" optional="true" type="integer" label="VARIANT MAX LENGTH" value="" help="Targeted VVariant maximum length to search for" />
45 </section>
46 </inputs>
47 <outputs>
48 <data name="out_gene_query" format="json" label="${tool.name} on ${on_string}: Gene Query" from_work_dir="gene_query_findings.json" />
49 </outputs>
50 <tests>
51 <test expect_num_outputs="1">
52 <param name="database" value="beacon" />
53 <param name="collection" value="genomicVariations" />
54 <param name="db_host" value="20.108.51.167" />
55 <param name="geneId" value="OR4F5-LOC729737" />
56 <param name="alternateBases" value="A" />
57 <param name="variantType" value="SNP" />
58 <param name="aminoacidChange" value="." />
59 <output name="out_gene_query">
60 <assert_contents><has_text_matching expression="_id"/></assert_contents>
61 </output>
62 </test>
63 </tests>
64 <help><![CDATA[
65 GeneId Queries are in essence a variation of Range Queries in which the coordinates are replaced by the HGNC gene symbol. It is left to the implementation if the matching is done on variants annotated for the gene symbol or if a positional translation is being applied.
66 ]]></help>
67 <expand macro="citations" />
68 </tool>