annotate macros.xml @ 1:d2646a23f6b2 draft

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

<macros>
    <token name="@VERSION_SUFFIX@">0</token>
    <token name="@TOOL_VERSION@">2.2.3</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">beacon2-import</requirement>
        </requirements>
    </xml>
    <xml name="xrefs">
        <xrefs>
            <xref type="bio.tools">ga4gh_beacon</xref>
        </xrefs>
    </xml>
    <xml name="creators">
        <creator>
            <person givenName="Khaled" familyName="Jum'ah" url="https://github.com/khaled196" />
            <person givenName="Björn" familyName="Grüning" url="https://github.com/bgruening" />
            <person givenName="Katarzyna" familyName="Kamieniecka" url="https://github.com/kkamieniecka" />
            <person givenName="Krzysztof" familyName="Poterlowicz" url="https://github.com/poterlowicz-lab" />
            <organization name="poterlowicz-lab" url="https://github.com/poterlowicz-lab" />
        </creator>
    </xml>
    <xml name="Connection_to_MongoDB">
        <param argument="--db-host" type="text" label="DATABASE HOST" value="127.0.0.1" help="Hostname/IP of the beacon database" />
        <param argument="--db-port" type="integer" label="DATABASE PORT" value="27017" help="Port of the beacon database" />
    </xml>
    <xml name="Database_Configuration">
        <param argument="--database" type="text" label="DATABASE" value="" help="The targeted beacon database" />
        <param argument="--collection" type="text" label="COLLECTION" value="" help="The targeted beacon collection from the desired database" />
    </xml>
    <xml name="citations">
        <citations>
            <citation type="doi">10.1002/humu.24369</citation>
        </citations>
    </xml>
    <xml name="configfile">
        <configfiles>
            <configfile name="credentials"><![CDATA[
            #set $db_auth_source = $__user__.extra_preferences.get('beacon2_account|db_auth_source', "")
            #set $db_user = $__user__.extra_preferences.get('beacon2_account|db_user', "")
            #set $db_password = $__user__.extra_preferences.get('beacon2_account|db_password', "")
            #if $db_user == "" or $db_password == "" or $db_auth_source == "":
                #set $db_auth_source = "admin"
                #set $db_user = "root"
                #set $db_password = "example"
            #end if
            {
                "db_auth_source": "$db_auth_source",
                "db_user": "$db_user",
                "db_password": "$db_password"
            }
            ]]></configfile>
    </configfiles>
    </xml>
</macros>