diff omero_roi_import.xml @ 0:9051b91545f6 draft

planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 5b1b30d409355cee98485815c1dd4ac48649bcc1

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/omero_roi_import.xml	Thu Sep 05 11:55:44 2024 +0000
@@ -0,0 +1,109 @@
+<tool id="omero_roi_import" name="OMERO ROI 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@">1</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 '$__tool_directory__/omero_roi_upload.py'  
+        --input_file '$input'  
+        --image_id $id  
+        --user '$__user__.extra_preferences.get("omero_account|username", $test_username)'  
+        --psw '$__user__.extra_preferences.get("omero_account|password", $test_password)'  
+        --host '$omero_host'  
+        --port $omero_port  
+        --log_file '$log'  
+    ]]></command>
+    <inputs>
+        <param argument="input" type="data" format="tabular" optional="false" label="Tab File with ROIs" help="Select ROIs Tabular file"/>
+        <param argument="id" type="integer" optional="false" label="Image ID where annotate the ROIs"/>
+        <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=""/>
+    </inputs>
+    <outputs>
+        <data name="log" format="txt"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="omero_host" value="host.docker.internal"/>
+            <param name="omero_port" value="6064"/>
+            <param name="id" value="1"/>
+            <param name="input" value="input_roi.tsv"/>
+            <param name="test_username" value="root"/>
+            <param name="test_password" value="omero"/>
+            <output name="log" value="output_table_roi.txt" ftype="txt">
+                <assert_contents>
+                    <has_text text="ROI ID: 7 for row 7"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help>
+
+Description
+-----------
+
+Tool to upload Regions of Interest (ROIs) to an OMERO server based on shape data provided
+in a tabular format (TSV file). The tool reads the shape information from the TSV file, creates the
+corresponding ROIs in OMERO, and links them to a specified image.
+
+**Column Headers**:
+
+        - shape, x, y, x_rad, y_rad, width, height, label, fontSize, x1, y1, x2, y2, points, fill_color, stroke_color, stroke_width, z, c, t, roi_name, roi_description
+
+- *Shape Type*:
+
+    The **shape** column indicates the type of shape being defined, such as Ellipse, Label, Line, Point, Polygon, Polyline, or Rectangle.
+
+- *Position and Dimensions*:
+
+    The columns **x**, **y**, **x_rad**, **y_rad**, **width**, and **height** specify the position and dimensions of the shapes, where applicable. For example, Ellipse uses x, y, x_rad, and y_rad, while Rectangle uses x, y, width, and height.
+
+- *Text Labels*:
+
+    The **label** and **fontSize** columns are used for the Label shape, specifying the text content and font size.
+
+- *Line Coordinates*:
+
+    The columns **x1**, **y1**, **x2**, and **y2** are used for defining the start and end points of a Line.
+
+- *Point Coordinates*:
+
+    The **points** column is used for defining multiple points in shapes like Polygon and Polyline. The points are listed as coordinate pairs.
+
+- *Colors*:
+
+    The **fill_color** and **stroke_color** columns define the fill and stroke colors of the shapes in RGBA format.
+
+- *Stroke Width*:
+
+    The **stroke_width** column specifies the width of the stroke or border around the shapes.
+
+- *Z, C, T Coordinates*:
+
+    The **z**, **c**, and **t** columns indicate the Z-plane, channel, and time point to which the shape is associated in the image stack.
+
+- *ROI Identification*:
+
+    The **roi_name** and **roi_description** columns provide a name and description for each ROI, allowing for easy identification and documentation within OMERO.
+
+    </help>
+    <citations>
+        <citation type="doi">10.1038/nmeth.1896</citation>
+    </citations>
+</tool>