annotate analyses.xml @ 1:2e057dfe494c draft

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

<tool id="beacon2_analyses" name="Beacon2 Analyses" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
    <description>َQuery the analyses collection in the beacon database for bioinformatic procedures to identify variants</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="creators"/>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[    
        beacon2-search analyses
        --db-host '$db_host'
        --db-port $db_port
        --database '$database'
        --collection '$collection'
        --advance-connection
        --db-auth-config '$credentials' 
        #if str($advanced_settings.aligner)
            --aligner '$advanced_settings.aligner'
        #end if
        #if str($advanced_settings.analysisDate)
            --analysisDate '$advanced_settings.analysisDate'
        #end if
        #if str($advanced_settings.biosampleId)
            --biosampleId '$advanced_settings.biosampleId'
        #end if
        #if str($advanced_settings.identification)
            --identification '$advanced_settings.identification'
        #end if
        #if str($advanced_settings.individualId)
            --individualId '$advanced_settings.individualId'
        #end if
        #if str($advanced_settings.pipelineName)
            --pipelineName '$advanced_settings.pipelineName'
        #end if
        #if str($advanced_settings.pipelineRef)
            --pipelineRef '$advanced_settings.pipelineRef'
        #end if
        #if str($advanced_settings.runId)
            --runId '$advanced_settings.runId'
        #end if
        #if str($advanced_settings.variantCaller)
            --variantCaller '$advanced_settings.variantCaller'
        #end if
        > analyses_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="--aligner" optional="true" type="text" label="ALIGNER" value="" help="Reference to mapping/alignment software. Example bwa-0.7.8" />
            <param argument="--analysisDate" optional="true" type="text" label="ANALYSIS DATE" value="" help="Date at which analysis was performed. Example 2021-10-17	 " />
            <param argument="--biosampleId" optional="true" type="text" label="BIOSAMPLE ID" value="" help="Reference to the id of the biosample this analysis is reporting on. Example S0001 " />
            <param argument="--identification" optional="true" type="text" label="ID" value="" help="Analysis reference ID (external accession or internal ID). Example GA.01234abcde" />
            <param argument="--individualId" optional="true" type="text" label="INDIVIDUALID" value="" help="Reference to the id of the individual this analysis is reporting on.	Example P0001 " />
            <param argument="--pipelineName" optional="true" type="text" label="PIPELINE NAME" value="" help="Analysis pipeline and version if a standardized pipeline was used. Example Pipeline-panel-0001-v1	 " />
            <param argument="--pipelineRef" optional="true" type="text" label="PIPELINE REF" value="" help="Link to Analysis pipeline resource" />
            <param argument="--runId" optional="true" type="text" label="RUNID" value="" help="	Run identifier (external accession or internal ID). Example SRR10903401" />
            <param argument="--variantCaller" optional="true" type="text" label="VARIANT CALLER" value="" help="Reference to variant calling software / pipeline. Example GATK4.0 " />
        </section>
    </inputs>
    <outputs>
        <data name="out_analyses_query" format="json" label="${tool.name} on ${on_string}: Analyses Query" from_work_dir="analyses_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="individualId" value="NA24694" />
            <param name="biosampleId" value="S0002" />
            <param name="aligner" value="bwa-0.7.8" />
            <param name="pipelineName" value="GATK Pipeline 4.2.3.0" />
            <param name="identification" value="refvar-66bf2f3c0db372483f7bd37b" />
            <output name="out_analyses_query">
                <assert_contents><has_text_matching expression="_id"/></assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
        Beacon2 Analyses queries the analyses collection in the Beacon database to identify bioinformatic procedures and variants. This tool allows detailed queries using advanced settings such as aligner, analysis date, biosample ID, and more.
    ]]></help>
    <expand macro="citations" />
</tool>