annotate macros.xml @ 5:18b86dcdd421 draft

planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit d69e684236ce5d36a09e84f1eae6d8c98ed7499b

<macros>
    <!-- for historic reasons the omero-py version is used as the version for all tools -->
    <token name="@TOOL_VERSION@">5.18.0</token>
    <token name="@EZOMERO_VERSION@">3.0.1</token>
    <token name="@PROFILE@">23.0</token>

    <xml name="ezomero_requirements">
        <requirements>
            <requirement type="package" version="@EZOMERO_VERSION@">ezomero</requirement>
            <requirement type="package" version="2.2.2">pandas</requirement>
            <yield/>
        </requirements>
    </xml>

    <xml name="omeropy_requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">omero-py</requirement>
            <!-- openjdk is needed: https://github.com/conda-forge/omero-py-feedstock/pull/16 -->
            <requirement type="package" version="21.0.2">openjdk</requirement>
            <yield/>
        </requirements>
    </xml>
    

    <xml name="host_port">
        <param name="omero_host" type="text" label="OMERO host URL">
            <validator type="regex" message="Enter a valid host location, for example, your.omero.server">^[a-zA-Z0-9._-]*$</validator>
            <validator type="expression" message="No two dots (..) allowed">'..' not in value</validator>
        </param>
        <param argument="omero_port" type="integer" optional="false" value="4064" label="OMERO port"/>
        <param name="test_username" type="hidden" value=""/>
        <param name="test_password" type="hidden" value=""/>
    </xml>
    <token name="@HOST_PORT@">
        --host '$omero_host'
        --port $omero_port
    </token>

    <xml name="credentials">
        <configfile name="credentials"><![CDATA[
{
    "username": "$__user__.extra_preferences.get('omero_account|username', $test_username)",
    "password": "$__user__.extra_preferences.get('omero_account|password', $test_password)"
}
        ]]></configfile>
    </xml>

    <token name="@SECURITY_DISCLAIMER@">
    **OMERO-suite Security Diclaimer:** To utilize the OMERO tools, the user must trust Galaxy instances.
    The configuration file, which contains your OMERO password and username, is stored in the job working directory.
    This directory only exists during the runtime of the job and should only be accessible by the system user that runs the job.
    However, please be aware that your username and password may be exposed to users with administrative rights.
    We are working on increasing the security of the OMERO suite
    </token>

</macros>