annotate cnv.xml @ 1:997f15134095 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit 23f6d9e5e91c43d5ab68e604205e06785635f42f

<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>