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comparison analyses.xml @ 0:e0ef4541078e 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 12:33:38 +0000
parents
children 681efbe99382
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1 <tool id="beacon2_analyses" name="Beacon2 Analyses" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
2 <description>ŁŽQuery the analyses collection in the beacon database for bioinformatic procedures to identify variants</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 analyses
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($advanced_settings.aligner)
17 --aligner '$advanced_settings.aligner'
18 #end if
19 #if str($advanced_settings.analysisDate)
20 --analysisDate '$advanced_settings.analysisDate'
21 #end if
22 #if str($advanced_settings.biosampleId)
23 --biosampleId '$advanced_settings.biosampleId'
24 #end if
25 #if str($advanced_settings.identification)
26 --identification '$advanced_settings.identification'
27 #end if
28 #if str($advanced_settings.individualId)
29 --individualId '$advanced_settings.individualId'
30 #end if
31 #if str($advanced_settings.pipelineName)
32 --pipelineName '$advanced_settings.pipelineName'
33 #end if
34 #if str($advanced_settings.pipelineRef)
35 --pipelineRef '$advanced_settings.pipelineRef'
36 #end if
37 #if str($advanced_settings.runId)
38 --runId '$advanced_settings.runId'
39 #end if
40 #if str($advanced_settings.variantCaller)
41 --variantCaller '$advanced_settings.variantCaller'
42 #end if
43 > analyses_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="--aligner" optional="true" type="text" label="ALIGNER" value="" help="Reference to mapping/alignment software. Example bwa-0.7.8" />
51 <param argument="--analysisDate" optional="true" type="text" label="ANALYSIS DATE" value="" help="Date at which analysis was performed. Example 2021-10-17 " />
52 <param argument="--biosampleId" optional="true" type="text" label="BIOSAMPLE ID" value="" help="Reference to the id of the biosample this analysis is reporting on. Example S0001 " />
53 <param argument="--identification" optional="true" type="text" label="ID" value="" help="Analysis reference ID (external accession or internal ID). Example GA.01234abcde" />
54 <param argument="--individualId" optional="true" type="text" label="INDIVIDUALID" value="" help="Reference to the id of the individual this analysis is reporting on. Example P0001 " />
55 <param argument="--pipelineName" optional="true" type="text" label="PIPELINE NAME" value="" help="Analysis pipeline and version if a standardized pipeline was used. Example Pipeline-panel-0001-v1 " />
56 <param argument="--pipelineRef" optional="true" type="text" label="PIPELINE REF" value="" help="Link to Analysis pipeline resource" />
57 <param argument="--runId" optional="true" type="text" label="RUNID" value="" help=" Run identifier (external accession or internal ID). Example SRR10903401" />
58 <param argument="--variantCaller" optional="true" type="text" label="VARIANT CALLER" value="" help="Reference to variant calling software / pipeline. Example GATK4.0 " />
59 </section>
60 </inputs>
61 <outputs>
62 <data name="out_analyses_query" format="json" label="${tool.name} on ${on_string}: Analyses Query" from_work_dir="analyses_query_findings.json" />
63 </outputs>
64 <tests>
65 <test expect_num_outputs="1">
66 <param name="database" value="beacon" />
67 <param name="collection" value="analyses" />
68 <param name="db_host" value="20.108.51.167" />
69 <param name="individualId" value="NA24694" />
70 <param name="biosampleId" value="S0002" />
71 <param name="aligner" value="bwa-0.7.8" />
72 <param name="pipelineName" value="GATK Pipeline 4.2.3.0" />
73 <param name="identification" value="refvar-668fc705ef8bca245c3c2185" />
74 <output name="out_analyses_query">
75 <assert_contents><has_text_matching expression="_id"/></assert_contents>
76 </output>
77 </test>
78 </tests>
79 <help><![CDATA[
80 Beacon2 Analyses queries the analyses collection in the Beacon database to identify bioinformatic procedures and variants. This tool allows detailed queries using advanced settings such as aligner, analysis date, biosample ID, and more.
81 ]]></help>
82 <expand macro="citations" />
83 </tool>