annotate 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

<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>