view sequence.xml @ 0:ad5a4a77ca9d draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258

<tool id="beacon2_sequence" name="Beacon2 Sequence" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
    <description>َQuery for the existence of a specified sequence at a given genomic position</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="creators"/>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[    
        beacon2-search sequence
        --db-host '$db_host'
        --db-port $db_port
        --database '$database'
        --collection '$collection'
        --advance-connection
        --db-auth-config '$credentials' 
        --alternateBases '$alternateBases'
        --referenceBases '$referenceBases'
        #if str($advanced_settings.referenceName)
            --referenceName '$advanced_settings.referenceName'
        #end if
        #if str($advanced_settings.start)
            --start $advanced_settings.start
        #end if
        #if str($advanced_settings.collectionIds)
            --collectionIds '$advanced_settings.collectionIds'
        #end if
        > sequenced_query_findings.json
    ]]></command>
    <expand macro="configfile"/>
    <inputs>
        <expand macro="Connection_to_MongoDB" />
        <expand macro="Database_Configuration" />
        <param argument="--alternateBases" type="text" label="Alternate bases" value="" help="" />
        <param argument="--referenceBases" type="text" label="Reference bases" value="" help="" />
        <section name="advanced_settings" title="Advanced settings" expanded="false">
            <param argument="--referenceName" optional="true" type="text" label="REFERENCENAME" value="" help="Reference name in numbers chr1/1, chr2/2, chr3/3, etc." />
            <param argument="--start" optional="true" type="integer" label="START" value="" help="Start position" />
            <param argument="--collectionIds"  optional="true" type="text" label="Collection ID" value="" help="Datasets ID" />
        </section>
    </inputs>
    <outputs>
        <data name="out_sequence_query" format="json" label="${tool.name} on ${on_string}: Sequence Query" from_work_dir="sequenced_query_findings.json" />
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <param name="database" value="beacon" />
            <param name="collection" value="genomicVariations" />
            <param name="db_host" value="20.108.51.167" />
            <param name="start" value="10176" />
            <param name="alternateBases" value="AC" />
            <param name="referenceBases" value="A" />
            <output name="out_sequence_query">
                <assert_contents><has_text_matching expression="_id"/></assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
        Sequence Queries query for the existence of a specified sequence at a given genomic position. Such queries correspond to the original Beacon queries and are used to match short, precisely defined genomic variants such as SNVs and INDELs.
    ]]></help>
    <expand macro="citations" />
</tool>