annotate omero_get_id.xml @ 2:c7b2650718fe draft default tip

planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 636cbb62d59819caca5bc9eab0a8ec31be5bdd46

<tool id="omero_get_id" name="OMERO get IDs" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT">
    <description> with ezomero </description>
    <macros>
        <import>macros.xml</import>
        <token name="@VERSION_SUFFIX@">0</token>
    </macros>
    <xrefs>
        <xref type="bio.tools">omero</xref>
    </xrefs>
    <expand macro="ezomero_requirements"/>
    <command detect_errors="exit_code"><![CDATA[
        python '$__tool_directory__'/omero_get_id.py
        --credential-file '$credentials'
        @HOST_PORT@
        --final_obj_type '$cond_obj_type.final_obj_type'
        --parent_obj_type '$cond_obj_type.parent_obj_type'
        --parent_id $cond_obj_type.parent_id
        --tsv_file '$tsv'
    ]]></command>
    <configfiles>
        <expand macro="credentials"/>
    </configfiles>
    <inputs>
        <expand macro="host_port"/>
        <conditional name="cond_obj_type">
            <param argument="final_obj_type" type="select" optional="false" label="Type of object to fetch ID:">
                <option value="Project">All Project IDs</option>
                <option value="Dataset">Dataset IDs</option>
                <option value="Image">Image IDs</option>
                <option value="Annotation">Annotation IDs (key values)</option>
                <option value="Tag">Tag IDs</option>
                <option value="Roi">ROI IDs</option>
                <option value="Table">Table IDs</option>
            </param>
            <when value="Project">
                <param name="parent_obj_type" type="hidden" value="All"/>
                <param name="parent_id" type="hidden" value="0"/>
            </when>
            <when value="Dataset">
                <param name="parent_obj_type" type="select" label="Which datasets?">
                    <option value="All">All datasets</option>
                    <option value="Project">Only datasets from a Project</option>
                </param>
                <param name="parent_id" type="integer" value="0" optional="false" label="ID of the project (leave 0 if you selected All)."/>
            </when>
            <when value="Image">
                <param name="parent_obj_type" type="select" label="Which images?">
                    <option value="All">All images</option>
                    <option value="Project">Only images from a Project</option>
                    <option value="Dataset">Only images from a Dataset</option>
                    <option value="Plate">Only images from a Plate</option>
                    <option value="Well">Only images from a Well</option>
                </param>
                <param name="parent_id" type="integer" value="0" optional="false" label="ID of the parent object above (leave 0 if you selected All)."/>
            </when>
            <when value="Annotation">
                <param name="parent_obj_type" type="select" label="Of which type of object?">
                    <option value="Project">Annotations from a Project</option>
                    <option value="Dataset">Annotations from a Dataset</option>
                    <option value="Plate">Annotations from a Plate</option>
                    <option value="Well">Annotations from a Well</option>
                    <option value="Image">Annotations from an Image</option>
                </param>
                <param name="parent_id" type="integer" value="0" optional="false" label="ID of the object above."/>
            </when>
            <when value="Tag">
                <param name="parent_obj_type" type="select" label="Of which type of object?">
                    <option value="Project">Tags from a Project</option>
                    <option value="Dataset">Tags from a Dataset</option>
                    <option value="Plate">Tags from a Plate</option>
                    <option value="Well">Tags from a Well</option>
                    <option value="Image">Tags from an Image</option>
                </param>
                <param name="parent_id" type="integer" value="0" optional="false" label="ID of the object above."/>
            </when>
            <when value="Roi">
                <param name="parent_obj_type" type="hidden" value="Image"/>
                <param name="parent_id" type="integer" value="0" optional="false" label="ID of the image from which you want to get ROI IDs."/>
            </when>
            <when value="Table">
                <param name="parent_obj_type" type="select" label="Of which type of object?">
                    <option value="Project">Table from a Project</option>
                    <option value="Dataset">Table from a Dataset</option>
                    <option value="Plate">Table from a Plate</option>
                    <option value="Well">Table from a Well</option>
                    <option value="Image">Table from an Image</option>
                </param>
                <param name="parent_id" type="integer" value="0" optional="false" label="ID of the object above."/>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="tsv" format="tabular"/>
    </outputs>
    <tests>
        <test>
            <param name="omero_host" value="host.docker.internal"/>
            <param name="omero_port" value="6064"/>
            <conditional name="cond_obj_type">
                <param name="final_obj_type" value="Project"/>
            </conditional>
            <param name="test_username" value="root"/>
            <param name="test_password" value="omero"/>
            <output name="tsv" value="output_ids_project.tsv" ftype="tabular">
                <assert_contents>
                    <has_text text="1"/>
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="omero_host" value="host.docker.internal"/>
            <param name="omero_port" value="6064"/>
            <conditional name="cond_obj_type">
                <param name="final_obj_type" value="Dataset"/>
                <param name="parent_obj_type" value="Project"/>
                <param name="parent_id" value="1"/>
            </conditional>
            <param name="test_username" value="root"/>
            <param name="test_password" value="omero"/>
            <output name="tsv" value="output_ids_dataset.tsv" ftype="tabular">
                <assert_contents>
                    <has_text text="1"/>
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="omero_host" value="host.docker.internal"/>
            <param name="omero_port" value="6064"/>
            <conditional name="cond_obj_type">
                <param name="final_obj_type" value="Image"/>
                <param name="parent_obj_type" value="Dataset"/>
                <param name="parent_id" value="1"/>
            </conditional>
            <param name="test_username" value="root"/>
            <param name="test_password" value="omero"/>
            <output name="tsv" value="output_ids_image.tsv" ftype="tabular">
                <assert_contents>
                    <has_text text="1"/>
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="omero_host" value="host.docker.internal"/>
            <param name="omero_port" value="6064"/>
            <conditional name="cond_obj_type">
                <param name="final_obj_type" value="Tag"/>
                <param name="parent_obj_type" value="Image"/>
                <param name="parent_id" value="1"/>
            </conditional>
            <param name="test_username" value="root"/>
            <param name="test_password" value="omero"/>
            <output name="tsv" ftype="tabular">
                <assert_contents>
                    <has_text text="1"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help>
Description
-----------

Tool to fetch project, dataset, images, annotations, tags, table and ROIs IDs user defined OMERO.server.

**Options**:

Project -> Project IDs present in the OMERO.server

Dataset -> Dataset IDs present in a specific Project or in the server

Image -> Image IDs present in a specific Dataset or Project or Well or Plate or in the server

Annotation (Key-Value Pairs) -> Annotation IDs linked to an Image or Dataset or Project or Well or Plate

Tag -> Tag IDs linked to an Image or Dataset or Project or Well or Plate

ROI -> ROI IDs linked to an Image

Table -> Table linked to an Image or Dataset or Project or Well or Plate

@SECURITY_DISCLAIMER@
    </help>
    <citations>
        <citation type="doi">10.1038/nmeth.1896</citation>
    </citations>
</tool>