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comparison runs.xml @ 0:34814a1b0a3f 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 12:37:26 +0000
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children 016fc58daa80
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-1:000000000000 0:34814a1b0a3f
1 <tool id="beacon2_runs" name="Beacon2 Runs" version="1.0.0" profile="21.05">
2 <description>Query the runs collection in 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">
9 <![CDATA[
10 beacon2-search runs
11 --db-host '$db_host'
12 --db-port $db_port
13 --database '$database'
14 --collection '$collection'
15 --advance-connection
16 --db-auth-config '$credentials'
17 #if str($advanced_settings.identification)
18 --identification '$advanced_settings.identification'
19 #end if
20 #if str($advanced_settings.individualId)
21 --individualId '$advanced_settings.individualId'
22 #end if
23 #if str($advanced_settings.libraryLayout)
24 --libraryLayout '$advanced_settings.libraryLayout'
25 #end if
26 #if str($advanced_settings.librarySelection)
27 --librarySelection '$advanced_settings.librarySelection'
28 #end if
29 #if str($advanced_settings.librarySource)
30 --librarySource '$advanced_settings.librarySource'
31 #end if
32 #if str($advanced_settings.libraryStrategy)
33 --libraryStrategy '$advanced_settings.libraryStrategy'
34 #end if
35 #if str($advanced_settings.platform)
36 --platform '$advanced_settings.platform'
37 #end if
38 #if str($advanced_settings.platformModel)
39 --platformModel '$advanced_settings.platformModel'
40 #end if
41 #if str($advanced_settings.runDate)
42 --runDate '$advanced_settings.runDate'
43 #end if
44 > runs_query_findings.json
45 ]]>
46 </command>
47 <expand macro="configfile"/>
48 <inputs>
49 <expand macro="Connection_to_MongoDB"/>
50 <expand macro="Database_Configuration"/>
51 <section name="advanced_settings" title="Advanced settings" expanded="false">
52 <param argument="--identification" optional="true" type="text" label="ID" value="" help="Run ID" />
53 <param argument="--individualId" optional="true" type="text" label="INDIVIDUAL ID" value="" help="Reference to the individual ID, e.g. TCGA-AO-A0JJ" />
54 <param argument="--libraryLayout" optional="true" type="text" label="LIBRARY LAYOUT" value="" help="Ontology value for the library layout e.g 'PAIRED', 'SINGLE'" />
55 <param argument="--librarySelection" optional="true" type="text" label="LIBRARY SELECTION" value="" help="Selection method for library preparation, e.g 'RANDOM', 'RT-PCR'" />
56 <param argument="--librarySource" optional="true" type="text" label="LIBRARY SOURCE" value="" help="Ontology value for the source of the sequencing or hybridization library, e.g 'genomic source', 'transcriptomic source'" />
57 <param argument="--libraryStrategy" optional="true" type="text" label="LIBRARY STRATEGY" value="" help="Library strategy, e.g. 'WGS'" />
58 <param argument="--platform" optional="true" type="text" label="PLATFORM" value="" help="General platform technology label where the specific model is not relevant, e.g. Illumina" />
59 <param argument="--platformModel" optional="true" type="text" label="PLATFORM MODEL" value="" help="Ontology value for experimental platform or methodology used, e.g. 'Illumina HiSeq 3000'" />
60 <param argument="--runDate" optional="true" type="text" label="RUN DATE" value="" help="Date at which the experiment was performed" />
61 </section>
62 </inputs>
63 <outputs>
64 <data name="out_runs_query" format="json" label="${tool.name} on ${on_string}: Runs Query" from_work_dir="runs_query_findings.json" />
65 </outputs>
66 <tests>
67 <test expect_num_outputs="1">
68 <param name="database" value="beacon" />
69 <param name="collection" value="runs" />
70 <param name="db_host" value="20.108.51.167" />
71 <param name="platform" value="Illumina " />
72 <param name="platformModel" value="2017-04-30" />
73 <param name="librarySource" value="KAPA library quantification kit" />
74 <param name="libraryLayout" value="PAIRED" />
75 <output name="out_runs_query">
76 <assert_contents>
77 <has_text_matching expression="_id"/>
78 </assert_contents>
79 </output>
80 </test>
81 </tests>
82 <help><![CDATA[
83 Beacon2 Runs queries the runs collection in the Beacon database for details on procedures used for sequencing a biosample.
84 ]]></help>
85 <expand macro="citations" />
86 </tool>