Mercurial > repos > iuc > beacon2_cnv
view cnv.xml @ 1:997f15134095 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit 23f6d9e5e91c43d5ab68e604205e06785635f42f
author | iuc |
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date | Mon, 19 Aug 2024 10:50:07 +0000 |
parents | 25424cc216f9 |
children | 398000f8de7d |
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<tool id="beacon2_cnv" name="Beacon2 CNV" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> <description>Retrieve the copy number varients from genomicVariations collection from the beacon database</description> <macros> <import>macros.xml</import> </macros> <expand macro="creators"/> <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ beacon2-search cnv --db-host '$db_host' --db-port $db_port --database '$database' --collection '$collection' --advance-connection --db-auth-config '$credentials' #if str($advanced_settings.variantInternalId) --variantInternalId '$advanced_settings.variantInternalId' #end if #if str($advanced_settings.analysisId) --analysisId '$advanced_settings.analysisId' #end if #if str($advanced_settings.individualId) --individualId '$advanced_settings.individualId' #end if #if str($advanced_settings.start) --start $advanced_settings.start #end if #if str($advanced_settings.end) --end $advanced_settings.end #end if #if str($advanced_settings.chromosome) --chromosome '$advanced_settings.chromosome' #end if #if str($advanced_settings.variantStateId) and $advanced_settings.variantStateId != "" --variantStateId '$advanced_settings.variantStateId' #end if #if str($advanced_settings.sequenceId) --sequenceId '$advanced_settings.sequenceId' #end if #if str($advanced_settings.variantType) --variantType '$advanced_settings.variantType' #end if #if str($advanced_settings.primarySite) --primarySite '$advanced_settings.primarySite' #end if #if str($advanced_settings.diseaseType) --diseaseType '$advanced_settings.diseaseType' #end if #if str($advanced_settings.gene) --gene '$advanced_settings.gene' #end if > cnv_query_findings.json ]]></command> <expand macro="configfile"/> <inputs> <expand macro="Connection_to_MongoDB" /> <expand macro="Database_Configuration" /> <section name="advanced_settings" title="Advanced settings" expanded="false"> <param argument="--variantInternalId" optional="true" type="text" label="VARIANT INTERNAL ID" value="" help="E.g. 11:52900000-134452384:DEL" /> <param argument="--analysisId" optional="true" type="text" label="ANALYSIS ID" value="" help="" /> <param argument="--individualId" optional="true" type="text" label="INDIVIDUAL ID" value="" help="" /> <param argument="--start" optional="true" type="integer" label="START" value="" help="Start position" /> <param argument="--end" optional="true" type="integer" label="END" value="" help="End position" /> <param argument="--chromosome" optional="true" type="text" label="CHROMOSOME" value="" help="Chromosome numbers (without chr)" /> <param argument="variantStateId" optional="true" type="select" label="GENDERS" help=""> <option value="EFO:0030070">EFO:0030070: copy number gain</option> <option value="EFO:0030071">EFO:0030071: low-level copy number gain</option> <option value="EFO:0030072">EFO:0030072: high-level copy number gain</option> <option value="EFO:0030073">EFO:0030073: focal genome amplification</option> <option value="EFO:0030067">EFO:0030067: copy number loss</option> <option value="EFO:0030068">EFO:0030068: low-level copy number loss</option> <option value="EFO:0020073">EFO:0020073: high-level copy number loss</option> <option value="EFO:0030069">EFO:0030069: complete genomic deletion</option> <option value="" selected="True">non specific</option> </param> <param argument="--sequenceId" optional="true" type="text" label="SEQUENCE ID" value="" help="E.g. refseq:NC_000011.10" /> <param argument="--gene" optional="true" type="text" label="GENE NAME" value="" help="Gene name e.g. 'AL645728.1'" /> <param argument="--variantType" optional="true" type="text" label="VARIANT TYPE" value="" help="Variant Type 'DEL' or 'DUP'" /> <param argument="--primarySite" optional="true" type="text" label="PRIMARY SITE" value="" help="Primary Site, e.g. 'brain'" /> <param argument="--diseaseType" optional="true" type="text" label="DISEASE TYPE" value="" help="Disease Type, e.g. 'adnexal and skin appendage neoplasms'" /> </section> </inputs> <outputs> <data name="out_cnv_query" format="json" label="${tool.name} on ${on_string}: CNV Query" from_work_dir="cnv_query_findings.json" /> </outputs> <tests> <test expect_num_outputs="1"> <param name="database" value="beacon" /> <param name="collection" value="test" /> <param name="db_host" value="20.108.51.167" /> <param name="chromosome" value="17" /> <param name="start" value="43044295" /> <param name="end" value="43170245" /> <param name="primarySite" value="breast" /> <param name="diseaseType" value="adnexal and skin appendage neoplasms" /> <param name="gene" value="BRCA1" /> <param name="variantStateId" value="EFO:0030068" /> <output name="out_cnv_query"> <assert_contents><has_text_matching expression="_id"/></assert_contents> </output> </test> </tests> <help><![CDATA[ Beacon CNV Queries are supposed to return matches of any copy number variants with at least partial overlap of the input parameters ]]></help> <expand macro="citations" /> </tool>