annotate omero_get_children_ids.xml @ 1:82f2efb46200 draft default tip

planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/omero_get_children_ids commit 3a5c830ad68e29c5e9f91edffa0a548c77aac141

<tool id="omero_get_children_ids" name="Omero" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01" license="MIT">
    <description>Get children ids</description>
    <macros>
        <token name="@TOOL_VERSION@">0.2.0</token>
        <token name="@VERSION_SUFFIX@">0</token>
    </macros>
    <requirements>
        <requirement type="package" version="5.17.0">omero-py</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        #if $omero_instance_type.omero_instance == "priv":
            ## the user wants to use a non-public OMERO instance
            ## check if credentials are set in the user-preferences, if not warn the user and exit
            #set $username = $__user__.extra_preferences.get('omero_account|username', "")
            #set $password = $__user__.extra_preferences.get('omero_account|password', "")

            #if $omero_instance_type.galaxy_test_param != 'true' and ($username == "" or $password ==""):
                echo "OMERO connection credentials are empty. Set your credentials via: User -> Preferences -> Manage Information" 1>&2 &&
                exit 1 &&
            #end if
        #end if
        python '$__tool_directory__/omero_get_children_ids.py'
        #if $omero_instance_type.omero_instance =='priv':
            -oh '$omero_instance_type.omero_host'
            $omero_instance_type.omero_secured
            -cf '$credentials'
        #end if
        --parent-object-type '$omero_object.parent_object_type'
        --omero-id '$omero_object.omero_id'
        --final-object-type '$omero_object.final_object_type'
        --output '$output'
        $get_name
    ]]></command>
    <configfiles>
        <configfile name="credentials"><![CDATA[
#if $omero_instance_type.omero_instance =='priv' and $omero_instance_type.galaxy_test_param == 'true':
    ## as a test for a private instance we actually use a public instance, but with credentials
    #set $username = 'public'
    #set $password = 'public'
#else:
    #set $username = $__user__.extra_preferences.get('omero_account|username', "")
    #set $password = $__user__.extra_preferences.get('omero_account|password', "")
#end if
{
    "username": "$username",
    "password": "$password"
}
        ]]></configfile>
    </configfiles>
    <inputs>
        <conditional name="omero_instance_type">
            <param name="omero_instance" type="select" label="Which OMERO instance to connect?"
                   help="By default, the tool will request children ID from IDR. If you 
                   need to connect to your own instance, set your connection username and password from User->Preference->Manage Information" >
                <option value="idr">IDR</option>
                <option value="priv">other OMERO instance</option>
            </param>
            <when value="priv">
                <param name="omero_host" type="text" label="OMERO host URL">
                    <validator type="regex" message="Enter a valid host location, for example, your.omero.server">^[a-zA-Z0-9._-]*$</validator>
                    <validator type="expression" message="No two dots (..) allowed">'..' not in value</validator>
                </param>
                <param name="omero_secured" type="boolean" label="Secured connection?" checked="true" truevalue="--omero-secured" falsevalue=""
                        help="Select Yes if your OMERO instance is running with SSL, otherwise select No">
                </param>
                <param name="galaxy_test_param" type="hidden" value="false" />
            </when>
            <when value="idr" />
        </conditional>
        <conditional name="omero_object">
            <param name="parent_object_type" type="select" label="Type of parent object">
                <option value="well">Well</option>
                <option value="plate">Plate</option>
                <option value="screen">Screen</option>
                <option value="dataset">Dataset</option>
                <option value="project">Project</option>
            </param>
            <when value="well">
                <param name="omero_id" type="integer" value="" label="Well ID on omero" />
                <param name="final_object_type" type="hidden" value="image"/>
            </when>
            <when value="plate">
                <param name="omero_id" type="integer" value="" label="Plate ID on omero" />
                <param name="final_object_type" type="select" label="Type of children object for which you want the id">
                    <option value="image">All Omero Image Ids</option>
                    <option value="well">All Omero Well Ids</option>
                </param>
            </when>
            <when value="screen">
                <param name="omero_id" type="integer" value="" label="Screen ID on omero" />
                <param name="final_object_type" type="select" label="Type of children object for which you want the id">
                    <option value="image">All Omero Image Ids</option>
                    <option value="well">All Omero Well Ids</option>
                    <option value="plate">All Omero Plate Ids</option>
                </param>
            </when>
            <when value="dataset">
                <param name="omero_id" type="integer" value="" label="Dataset ID on omero" />
                <param name="final_object_type" type="hidden" value="image"/>
            </when>
            <when value="project">
                <param name="omero_id" type="integer" value="" label="Project ID on omero" />
                <param name="final_object_type" type="select" label="Type of children object for which you want the id">
                    <option value="image">All Omero Image Ids</option>
                    <option value="dataset">All Omero Dataset Ids</option>
                </param>
            </when>
        </conditional>
        <param name="get_name" type="boolean" truevalue="--get-name" falsevalue="" checked="false" label="Retrieve names into a second column" />
    </inputs>
    <outputs>
        <data name="output" format="tabular" label="All ${omero_object.final_object_type} from ${omero_object.parent_object_type} ID ${omero_object.omero_id}" />
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <conditional name="omero_instance_type">
                <param name="omero_instance" value="idr"/>
            </conditional>
            <conditional name="omero_object">
                <param name="parent_object_type" value="well"/>
                <param name="omero_id" value="2184933"/>
                <param name="final_object_type" value="image"/>
            </conditional>
            <output name="output">
                <assert_contents>
                    <has_line line="14263182"/>
                    <has_n_lines n="4"/>
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="1">
            <conditional name="omero_instance_type">
                <param name="omero_instance" value="idr"/>
            </conditional>
            <conditional name="omero_object">
                <param name="parent_object_type" value="well"/>
                <param name="omero_id" value="2184933"/>
                <param name="final_object_type" value="image"/>
            </conditional>
            <param name="get_name" value="true"/>
            <output name="output">
                <assert_contents>
                    <has_text text="003012001.flex [Well A-1; Field #1]"/>
                    <has_n_lines n="4"/>
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="1">
            <conditional name="omero_instance_type">
                <param name="omero_instance" value="idr"/>
            </conditional>
            <conditional name="omero_object">
                <param name="parent_object_type" value="plate"/>
                <param name="omero_id" value="10055"/>
                <param name="final_object_type" value="image"/>
            </conditional>
            <output name="output">
                <assert_contents>
                    <has_line line="14263182"/>
                    <has_n_lines n="1300"/>
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="1">
            <conditional name="omero_instance_type">
                <param name="omero_instance" value="idr"/>
            </conditional>
            <conditional name="omero_object">
                <param name="parent_object_type" value="plate"/>
                <param name="omero_id" value="10055"/>
                <param name="final_object_type" value="well"/>
            </conditional>
            <output name="output">
                <assert_contents>
                    <has_line line="2184933"/>
                    <has_n_lines n="325"/>
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="1">
            <conditional name="omero_instance_type">
                <param name="omero_instance" value="idr"/>
            </conditional>
            <conditional name="omero_object">
                <param name="parent_object_type" value="screen"/>
                <param name="omero_id" value="3302"/>
                <param name="final_object_type" value="image"/>
            </conditional>
            <output name="output">
                <assert_contents>
                    <has_line line="14263182"/>
                    <has_n_lines n="9100"/>
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="1">
            <conditional name="omero_instance_type">
                <param name="omero_instance" value="idr"/>
            </conditional>
            <conditional name="omero_object">
                <param name="parent_object_type" value="screen"/>
                <param name="omero_id" value="3302"/>
                <param name="final_object_type" value="plate"/>
            </conditional>
            <output name="output">
                <assert_contents>
                    <has_line line="10055"/>
                    <has_n_lines n="7"/>
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="1">
            <conditional name="omero_instance_type">
                <param name="omero_instance" value="idr"/>
            </conditional>
            <conditional name="omero_object">
                <param name="parent_object_type" value="screen"/>
                <param name="omero_id" value="3302"/>
                <param name="final_object_type" value="well"/>
            </conditional>
            <output name="output">
                <assert_contents>
                    <has_line line="2184933"/>
                    <has_n_lines n="2275"/>
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="1">
            <conditional name="omero_instance_type">
                <param name="omero_instance" value="idr"/>
            </conditional>
            <conditional name="omero_object">
                <param name="parent_object_type" value="dataset"/>
                <param name="omero_id" value="18101"/>
                <param name="final_object_type" value="image"/>
            </conditional>
            <output name="output">
                <assert_contents>
                    <has_line line="15148237"/>
                    <has_n_lines n="199"/>
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="1">
            <conditional name="omero_instance_type">
                <param name="omero_instance" value="idr"/>
            </conditional>
            <conditional name="omero_object">
                <param name="parent_object_type" value="project"/>
                <param name="omero_id" value="2801"/>
                <param name="final_object_type" value="image"/>
            </conditional>
            <output name="output">
                <assert_contents>
                    <has_line line="15148237"/>
                    <has_n_lines n="494"/>
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="1">
            <conditional name="omero_instance_type">
                <param name="omero_instance" value="idr"/>
            </conditional>
            <conditional name="omero_object">
                <param name="parent_object_type" value="project"/>
                <param name="omero_id" value="2801"/>
                <param name="final_object_type" value="dataset"/>
            </conditional>
            <output name="output">
                <assert_contents>
                    <has_line line="18101"/>
                    <has_n_lines n="2"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[

.. class:: infomark

**What it does**

This tool will create a file with the list of all children ids of a given omero object.

If the option is set, it can also retrive the names.

    ]]></help>
</tool>