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comparison cnv.xml @ 0:2dd335ce7dba 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 12:34:00 +0000
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children bb408389c342
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-1:000000000000 0:2dd335ce7dba
1 <tool id="beacon2_cnv" name="Beacon2 CNV" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
2 <description>Retrieve the copy number varients from genomicVariations collection from 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"><![CDATA[
9 beacon2-search cnv
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 #if str($advanced_settings.variantInternalId)
17 --variantInternalId '$advanced_settings.variantInternalId'
18 #end if
19 #if str($advanced_settings.analysisId)
20 --analysisId '$advanced_settings.analysisId'
21 #end if
22 #if str($advanced_settings.individualId)
23 --individualId '$advanced_settings.individualId'
24 #end if
25 #if str($advanced_settings.start)
26 --start $advanced_settings.start
27 #end if
28 #if str($advanced_settings.end)
29 --end $advanced_settings.end
30 #end if
31 #if str($advanced_settings.chromosome)
32 --chromosome '$advanced_settings.chromosome'
33 #end if
34 #if str($advanced_settings.variantStateId)
35 --variantStateId '$advanced_settings.variantStateId'
36 #end if
37 #if str($advanced_settings.variantState)
38 --variantState '$advanced_settings.variantState'
39 #end if
40 #if str($advanced_settings.sequenceId)
41 --sequenceId '$advanced_settings.sequenceId'
42 #end if
43 > cnv_query_findings.json
44 ]]></command>
45 <expand macro="configfile"/>
46 <inputs>
47 <expand macro="Connection_to_MongoDB" />
48 <expand macro="Database_Configuration" />
49 <section name="advanced_settings" title="Advanced settings" expanded="false">
50 <param argument="--variantInternalId" optional="true" type="text" label="VARIANT INTERNAL ID" value="" help="E.g. 11:52900000-134452384:DEL" />
51 <param argument="--analysisId" optional="true" type="text" label="ANALYSIS ID" value="" help="" />
52 <param argument="--individualId" optional="true" type="text" label="INDIVIDUAL ID" value="" help="" />
53 <param argument="--start" optional="true" type="integer" label="START" value="" help="Start position" />
54 <param argument="--end" optional="true" type="integer" label="END" value="" help="End position" />
55 <param argument="--chromosome" optional="true" type="text" label="CHROMOSOME" value="" help="Chromosome numbers (without chr)" />
56 <param argument="--variantStateId" optional="true" type="text" label="VARIANT STATE ID" value="" help="E.g EFO:0030067" />
57 <param argument="--variantState" optional="true" type="text" label="VARIANT STATE" value="" help="E.g. copy number loss" />
58 <param argument="--sequenceId" optional="true" type="text" label="SEQUENCE ID" value="" help="E.g. refseq:NC_000011.10" />
59 </section>
60 </inputs>
61 <outputs>
62 <data name="out_cnv_query" format="json" label="${tool.name} on ${on_string}: CNV Query" from_work_dir="cnv_query_findings.json" />
63 </outputs>
64 <tests>
65 <test expect_num_outputs="1">
66 <param name="database" value="beacon" />
67 <param name="collection" value="cnv" />
68 <param name="db_host" value="20.108.51.167" />
69 <param name="chromosome" value="1" />
70 <param name="start" value="243618689" />
71 <param name="end" value="243620819" />
72 <param name="variantStateId" value="EFO:0030068" />
73 <output name="out_cnv_query">
74 <assert_contents><has_text_matching expression="_id"/></assert_contents>
75 </output>
76 </test>
77 </tests>
78 <help><![CDATA[
79 Beacon CNV Queries are supposed to return matches of any copy number variants with at least partial overlap of the input parameters
80 ]]></help>
81 <expand macro="citations" />
82 </tool>