comparison omero_metadata_import.xml @ 3:eba4011643dd draft

planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2

2:e41f70e69349

<tool id="omero_metadata_import" name="OMERO Metadata Import" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"
      profile="20.01" license="MIT">
    <description> with ezomero </description>
    <macros>
        <token name="@TOOL_VERSION@">5.18.0</token>
        <token name="@VERSION_SUFFIX@">2</token>
    </macros>
    <xrefs>
        <xref type="bio.tools">omero</xref>
    </xrefs>
    <requirements>
        <requirement type="package" version="3.0.1">ezomero</requirement>
        <requirement type="package" version="2.2.2">pandas</requirement>
        <!-- openjdk is needed: https://github.com/conda-forge/omero-py-feedstock/pull/16 -->
        <requirement type="package" version="21.0.2">openjdk</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        python $__tool_directory__/omero_metadata_upload.py
        --credential-file '$credentials'
        --host $omero_host
        --port $omero_port
        --obj_type $obj_type
        --ann_type $ann_type
        --ann_file $ann_file
        --an_name $an_name
        --log_file $log
        #if $object_id_selection == "existing_object"
            --did "$did"
        #end if
    ]]></command>
    <configfiles>
        <configfile name="credentials"><![CDATA[
{
    "username": "$__user__.extra_preferences.get('omero_account|username', $test_username)",
    "password": "$__user__.extra_preferences.get('omero_account|password', $test_password)"
}
        ]]></configfile>
    </configfiles>
    <inputs>
        <param name="omero_host" type="text" label="OMERO host URL">
            <validator type="regex" message="Enter a valid host location, for example, your.omero.server">^[a-zA-Z0-9._-]*$</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 argument="obj_type" type="select" optional="true" label="Target Object Type">
            <option value="project">Project</option>
            <option value="screen">Screen</option>
            <option value="dataset">Dataset</option>
            <option value="image">Image</option>

            <option value="table">Table</option>
            <option value="KV">Key-Value Pairs</option>
        </param>
        <param argument="ann_file" type="data" format="tabular" optional="false" label="Annotation file" help="Select annotation file"/>
        <param argument="an_name" type="text" optional="false" label="Annotation Name"/>
        <param name="test_username" type="hidden" value=""/>
        <param name="test_password" type="hidden" value=""/>
    </inputs>
    <outputs>
        <data name="log" format="txt"/>
    </outputs>
    <tests>

3:eba4011643dd

<tool id="omero_metadata_import" name="OMERO Metadata Import" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT">
    <description> with ezomero </description>
    <macros>
        <import>macros.xml</import>
        <token name="@VERSION_SUFFIX@">3</token>
    </macros>
    <xrefs>
        <xref type="bio.tools">omero</xref>
    </xrefs>
    <expand macro="ezomero_requirements"/>
    <command detect_errors="exit_code"><![CDATA[
        python $__tool_directory__/omero_metadata_upload.py
        --credential-file '$credentials'
        @HOST_PORT@
        --obj_type $obj_type
        --ann_type $ann_type
        --ann_file $ann_file
        --an_name $an_name
        --log_file $log
        #if $object_id_selection == "existing_object"
            --did "$did"
        #end if
    ]]></command>
    <configfiles>
        <expand macro="credentials"/>
    </configfiles>
    <inputs>
        <expand macro="host_port"/>
        <param argument="obj_type" type="select" optional="true" label="Target Object Type">
            <option value="project">Project</option>
            <option value="screen">Screen</option>
            <option value="dataset">Dataset</option>
            <option value="image">Image</option>

            <option value="table">Table</option>
            <option value="KV">Key-Value Pairs</option>
        </param>
        <param argument="ann_file" type="data" format="tabular" optional="false" label="Annotation file" help="Select annotation file"/>
        <param argument="an_name" type="text" optional="false" label="Annotation Name"/>
    </inputs>
    <outputs>
        <data name="log" format="txt"/>
    </outputs>
    <tests>