annotate cohorts.xml @ 1:d524bd42b89e draft

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

<tool id="beacon2_cohorts" name="Beacon2 Cohorts" version="1.0.0" profile="21.05">
    <description>Query the Cohorts collection in the beacon database</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="creators"/>
    <expand macro="requirements"/>
    <command detect_errors="exit_code">
        <![CDATA[
        beacon2-search cohorts
        --db-host '$db_host'
        --db-port $db_port
        --database '$database'
        --collection '$collection'
        --advance-connection
        --db-auth-config '$credentials' 
        #if str($advanced_settings.cohortDataTypes)
            --cohortDataTypes '$advanced_settings.cohortDataTypes'
        #end if
        #if str($advanced_settings.cohortDesign)
            --cohortDesign '$advanced_settings.cohortDesign'
        #end if
        #if str($advanced_settings.cohortSize)
            --cohortSize $advanced_settings.cohortSize
        #end if
        #if str($advanced_settings.identification)
            --identification '$advanced_settings.identification'
        #end if
        #if str($advanced_settings.cohortType)
            --cohortType '$advanced_settings.cohortType'
        #end if
        #if str($advanced_settings.genders) and $advanced_settings.genders != ""
            --genders '$advanced_settings.genders'
        #end if
        #if str($advanced_settings.name)
            --name '$advanced_settings.name'
        #end if
        > cohorts_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="--cohortDataTypes" optional="true" type="text" label="COHORTDATA TYPES" value="" help="The type of data chorort, e.g. clinical history" />
            <param argument="--cohortDesign" optional="true" type="text" label="COHORTDESIGN" value="" help="A plan specification comprised of protocols that are executed as part of an investigation, e.g. longitudinal study design" />
            <param argument="--cohortSize" optional="true" type="integer" label="COHORT SIZE" value="" help="Count of unique Individuals in cohort" />
            <param argument="--cohortType" optional="true" type="text" label="COHORT TYPE" value="" help="Cohort type by its definition, e.g. study-defined" />
            <param argument="--identification" optional="true" type="text" label="ID" value="" help="Cohort identifier, e.g. cohort0001" />
            <param argument="--genders" optional="true" type="select" label="GENDERS" help="">
            <option value="male">male</option>
            <option value="female">female</option>
            <option value="" selected="True">non specific</option>
            </param>
            <param argument="--name" optional="true" type="text" label="NAME" value="" help="Name of the cohort" />
        </section>
    </inputs>
    <outputs>
        <data name="out_cohorts_query" format="json" label="${tool.name} on ${on_string}: Cohorts Query" from_work_dir="cohorts_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="cohortType" value="study-defined" />
            <param name="cohortDataTypes" value="demographic data" />
            <output name="out_cohorts_query">
                <assert_contents>
                    <has_text_matching expression="_id"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
        Beacon2 Cohorts queries the cohorts collection in the Beacon database to study the variants or individuals in a populations or  groups that share something in common.
    ]]></help>
    <expand macro="citations" />
</tool>