diff omero_dataset_to_plate.xml @ 0:5ad32d18fe82 draft

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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/omero_dataset_to_plate.xml	Mon Dec 16 20:56:16 2024 +0000
@@ -0,0 +1,67 @@
+<tool id="omero_dataset_to_plate" name="OMERO Dataset to Plate" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT">
+   <description> with omero-py </description>
+   <macros>
+       <import>macros.xml</import>
+       <token name="@VERSION_SUFFIX@">3</token>
+   </macros>
+   <xrefs>
+       <xref type="bio.tools">omero</xref>
+   </xrefs>
+   <expand macro="omeropy_requirements"/>
+   <command detect_errors="exit_code"><![CDATA[
+       python '$__tool_directory__/omero_dataset_to_plate.py'
+       --credential-file '$credentials'
+       @HOST_PORT@
+       --dataset_id '$dataset_id'
+       --log_file '$log'
+       --mapping_file '$mapping'
+       '$delete_dataset'
+   ]]></command>
+   <configfiles>
+       <expand macro="credentials"/>
+   </configfiles>
+   <inputs>
+       <expand macro="host_port"/>
+       <param name="dataset_id" type="integer" optional="false" min = "1" label="Dataset ID to convert to a plate"/>
+       <param name="mapping" type="data" format= "tabular" optional="false" label="Mapping file"/>
+       <param name="delete_dataset" type="boolean" truevalue="--delete_dataset" falsevalue="" checked="false" label="Delete Dataset" help="Delete dataset after import"/>
+   </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="dataset_id" value="2"/>
+           <param name="test_username" value="root"/>
+           <param name="test_password" value="omero"/>
+           <param name="mapping" value="mapping.tsv"/>
+           <param name="delete_dataset" value="True"/>
+           <output name="log" value="dataset_conversion_log.txt" ftype="txt">
+               <assert_contents>
+                   <has_text text="Images from Dataset 2 successfully added to Plate 1"/>
+               </assert_contents>
+           </output>
+       </test>
+   </tests>
+   <help>
+Description
+-----------
+- Tool to convert an existing dataset to a plate in OMERO
+- The tool is taking as input a mapping tabular file with Filename and Well Position:
+  +------------+---------------+
+  | Filename   | Well          |
+  +============+===============+
+  | image1.tiff| A2            |
+  +------------+---------------+
+  | image2.tiff| B5            |
+  +------------+---------------+
+  | image3.tiff| H12           |
+  +------------+---------------+
+@SECURITY_DISCLAIMER@
+   </help>
+   <citations>
+       <citation type="doi">10.1038/nmeth.1896</citation>
+   </citations>
+</tool>