omero_roi_import: omero_roi_import.xml comparison

comparison omero_roi_import.xml @ 2:4f4dc352d660 draft

planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 266752b0162fbdb32f132a6702cb661ae36f48f0

author	ufz
date	Thu, 12 Sep 2024 16:30:36 +0000
parents	e957793051a8
children	dfe0aae1495c

comparison

equal deleted inserted replaced

-:e957793051a8
+:4f4dc352d660
 <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@">2</token>
+<token name="@VERSION_SUFFIX@">3</token>
 </macros>
 <xrefs>
 <xref type="bio.tools">omero</xref>
 </xrefs>
 <requirements>
 <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", $test_username)'
+--credential-file '$credentials'
---psw '$__user__.extra_preferences.get("omero_account|password", $test_password)'
+--host '$omero_host'
---host '$omero_host'
+--port $omero_port
---port $omero_port
+--log_file '$log'
---log_file '$log'
 ]]></command>
+<configfiles>
+<configfile name="credentials"><![CDATA[
+{
+"username": "$__user__.extra_preferences.get('omero_account|username', $test_username)",
+"password": "$__user__.extra_preferences.get('omero_account|password', $test_password)"
+}
+]]></configfile>
+</configfiles>
 <inputs>
 <param argument="input" type="data" format="tabular" optional="false" label="Tab File with ROIs" help="Select ROIs Tabular file"/>
 <param argument="id" type="integer" value="" optional="false" label="Image ID where annotate the ROIs"/>
 <param name="omero_host" type="text" label="OMERO host URL">
 <validator type="regex" message="Enter a valid host location, for example, your.omero.server">^[a-zA-Z0-9._-]*$</validator>
 <assert_contents>
 <has_text text="ROI ID: 7 for row 7"/>
 </assert_contents>
 </output>
 </test>
+<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_minimal.tsv"/>
+<param name="test_username" value="root"/>
+<param name="test_password" value="omero"/>
+<output name="log" value="output_table_roi_minimal.txt" ftype="txt">
+<assert_contents>
+<has_text text="ROI ID: 8 for row 1"/>
+</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**:
+**Column Headers** (not all columns are required for all shapes):
 - 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*:
 - *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.
+- *Label*:
+Any ROI can be labelled using the column **label**, this label will appear on the OMERO web interface.
 - *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.
+The **points** column is used for defining multiple points in shapes like Polygon and Polyline. The points are listed as coordinate pairs, like '(300,300),(350,350),(300,400)'
 - *Colors*:
-The **fill_color** and **stroke_color** columns define the fill and stroke colors of the shapes in RGBA format.
+The **fill_color** and **stroke_color** columns define the fill and stroke colors of the shapes in RGBA format, like '(0,255,255,128)'.
 - *Stroke Width*:
 The **stroke_width** column specifies the width of the stroke or border around the shapes.
 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.
+The **roi_name** and **roi_description** columns provide a name and description for each ROI, allowing for easy identification and documentation within OMERO however they do not appear on the OMERO web interface.
 </help>
 <citations>
 <citation type="doi">10.1038/nmeth.1896</citation>
 </citations>

Mercurial > repos > ufz > omero_roi_import

comparison omero_roi_import.xml @ 2:4f4dc352d660 draft