comparison 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

0:b0876c73076b

<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@">0.1.0</token>
        <token name="@VERSION_SUFFIX@">0</token>
    </macros>
    <requirements>
        <requirement type="package" version="5.17.0">omero-py</requirement>
    </requirements>

        #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'
    ]]></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

                    <option value="image">All Omero Image Ids</option>
                    <option value="dataset">All Omero Dataset Ids</option>
                </param>
            </when>
        </conditional>
    </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="plate"/>
                <param name="omero_id" value="10055"/>
                <param name="final_object_type" value="image"/>
            </conditional>
            <output name="output">

**What it does**

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

    ]]></help>
</tool>

1:82f2efb46200

<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>

        #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

                    <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>
            <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">

**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>