annotate import.xml @ 1:d2646a23f6b2 draft

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

<tool id="beacon2_import" name="Beacon2 Import" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
    <description>Import JSON formatted datasets to beacon database</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="creators"/>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[    
        ln -s '$input_json_file' ./input.json &&
        beacon2-import
        --input_json_file ./input.json
        --db-host $db_host
        --db-port $db_port
        --database '$database'
        --collection '$collection'
        --advance-connection
        --db-auth-config '$credentials' 
        $advanced_settings.clearAll
        #if $advanced_settings.clearColl:
            $advanced_settings.clearColl
            --removeCollection $advanced_settings.removeCollection
        #end if 
        > logs.txt
    ]]></command>
    <expand macro="configfile"/>
    <inputs>
        <expand macro="Connection_to_MongoDB" />
        <expand macro="Database_Configuration" />
        <param argument="--input_json_file" type="data" format="json" label="INPUT JSON FILE" help="Input the local path to the JSON file or its name on your Galaxy History to import to beacon" />
        <section name="advanced_settings" title="Advanced settings" expanded="false">
            <param argument="--clearAll" type="boolean" checked="false" truevalue="--clearAll" falsevalue="" label="CLEAR ALL COLLECTIONS" help="Delete all data before the new import" />
            <param argument="--clearColl" type="boolean" checked="false" truevalue="--clearColl" falsevalue="" label="CLEAR SPECIFIC COLLECTION" help="Delete specific collection before the new import" />
            <param argument="--removeCollection"  optional="true" type="text" label="REMOVED COLLECTION NAME" value="" help="Define the collection name for deletion" />
        </section>
    </inputs>
    <outputs>
        <data name="out_logs" format="txt" label="${tool.name} on ${on_string}: Log file" from_work_dir="logs.txt" />
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <param name="input_json_file" ftype="json" value="HG00096.json" />
            <param name="db_host" value="20.108.51.167" />
            <param name="database" value="beacon" />
            <param name="collection" value="test" />
            <output name="out_logs">
                <assert_contents><has_text_matching expression="inserted"/></assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
        Import JSON formatted datasets to Beacon MongoDB
    ]]></help>
    <expand macro="citations" />
</tool>