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comparison cnv.xml @ 1:997f15134095 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit 23f6d9e5e91c43d5ab68e604205e06785635f42f
author iuc
date Mon, 19 Aug 2024 10:50:07 +0000
parents 25424cc216f9
children 398000f8de7d
comparison
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0:25424cc216f9 1:997f15134095
29 --end $advanced_settings.end 29 --end $advanced_settings.end
30 #end if 30 #end if
31 #if str($advanced_settings.chromosome) 31 #if str($advanced_settings.chromosome)
32 --chromosome '$advanced_settings.chromosome' 32 --chromosome '$advanced_settings.chromosome'
33 #end if 33 #end if
34 #if str($advanced_settings.variantStateId) 34 #if str($advanced_settings.variantStateId) and $advanced_settings.variantStateId != ""
35 --variantStateId '$advanced_settings.variantStateId' 35 --variantStateId '$advanced_settings.variantStateId'
36 #end if
37 #if str($advanced_settings.variantState)
38 --variantState '$advanced_settings.variantState'
39 #end if 36 #end if
40 #if str($advanced_settings.sequenceId) 37 #if str($advanced_settings.sequenceId)
41 --sequenceId '$advanced_settings.sequenceId' 38 --sequenceId '$advanced_settings.sequenceId'
39 #end if
40 #if str($advanced_settings.variantType)
41 --variantType '$advanced_settings.variantType'
42 #end if
43 #if str($advanced_settings.primarySite)
44 --primarySite '$advanced_settings.primarySite'
45 #end if
46 #if str($advanced_settings.diseaseType)
47 --diseaseType '$advanced_settings.diseaseType'
48 #end if
49 #if str($advanced_settings.gene)
50 --gene '$advanced_settings.gene'
42 #end if 51 #end if
43 > cnv_query_findings.json 52 > cnv_query_findings.json
44 ]]></command> 53 ]]></command>
45 <expand macro="configfile"/> 54 <expand macro="configfile"/>
46 <inputs> 55 <inputs>
51 <param argument="--analysisId" optional="true" type="text" label="ANALYSIS ID" value="" help="" /> 60 <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="" /> 61 <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" /> 62 <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" /> 63 <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)" /> 64 <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" /> 65 <param argument="variantStateId" optional="true" type="select" label="GENDERS" help="">
57 <param argument="--variantState" optional="true" type="text" label="VARIANT STATE" value="" help="E.g. copy number loss" /> 66 <option value="EFO:0030070">EFO:0030070: copy number gain</option>
67 <option value="EFO:0030071">EFO:0030071: low-level copy number gain</option>
68 <option value="EFO:0030072">EFO:0030072: high-level copy number gain</option>
69 <option value="EFO:0030073">EFO:0030073: focal genome amplification</option>
70 <option value="EFO:0030067">EFO:0030067: copy number loss</option>
71 <option value="EFO:0030068">EFO:0030068: low-level copy number loss</option>
72 <option value="EFO:0020073">EFO:0020073: high-level copy number loss</option>
73 <option value="EFO:0030069">EFO:0030069: complete genomic deletion</option>
74 <option value="" selected="True">non specific</option>
75 </param>
58 <param argument="--sequenceId" optional="true" type="text" label="SEQUENCE ID" value="" help="E.g. refseq:NC_000011.10" /> 76 <param argument="--sequenceId" optional="true" type="text" label="SEQUENCE ID" value="" help="E.g. refseq:NC_000011.10" />
77 <param argument="--gene" optional="true" type="text" label="GENE NAME" value="" help="Gene name e.g. 'AL645728.1'" />
78 <param argument="--variantType" optional="true" type="text" label="VARIANT TYPE" value="" help="Variant Type 'DEL' or 'DUP'" />
79 <param argument="--primarySite" optional="true" type="text" label="PRIMARY SITE" value="" help="Primary Site, e.g. 'brain'" />
80 <param argument="--diseaseType" optional="true" type="text" label="DISEASE TYPE" value="" help="Disease Type, e.g. 'adnexal and skin appendage neoplasms'" />
59 </section> 81 </section>
60 </inputs> 82 </inputs>
61 <outputs> 83 <outputs>
62 <data name="out_cnv_query" format="json" label="${tool.name} on ${on_string}: CNV Query" from_work_dir="cnv_query_findings.json" /> 84 <data name="out_cnv_query" format="json" label="${tool.name} on ${on_string}: CNV Query" from_work_dir="cnv_query_findings.json" />
63 </outputs> 85 </outputs>
64 <tests> 86 <tests>
65 <test expect_num_outputs="1"> 87 <test expect_num_outputs="1">
66 <param name="database" value="beacon" /> 88 <param name="database" value="beacon" />
67 <param name="collection" value="cnv" /> 89 <param name="collection" value="test" />
68 <param name="db_host" value="20.108.51.167" /> 90 <param name="db_host" value="20.108.51.167" />
69 <param name="chromosome" value="1" /> 91 <param name="chromosome" value="17" />
70 <param name="start" value="243618689" /> 92 <param name="start" value="43044295" />
71 <param name="end" value="243620819" /> 93 <param name="end" value="43170245" />
94 <param name="primarySite" value="breast" />
95 <param name="diseaseType" value="adnexal and skin appendage neoplasms" />
96 <param name="gene" value="BRCA1" />
72 <param name="variantStateId" value="EFO:0030068" /> 97 <param name="variantStateId" value="EFO:0030068" />
73 <output name="out_cnv_query"> 98 <output name="out_cnv_query">
74 <assert_contents><has_text_matching expression="_id"/></assert_contents> 99 <assert_contents><has_text_matching expression="_id"/></assert_contents>
75 </output> 100 </output>
76 </test> 101 </test>