Mercurial > repos > ufz > omero_metadata_import
diff omero_metadata_import.xml @ 0:352e9d4eaf70 draft
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit b9d952c8874f75f738ca4121d7e5274a7946035a
| author | ufz |
|---|---|
| date | Wed, 07 Aug 2024 12:54:19 +0000 |
| parents | |
| children | 588d6fa22fc4 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/omero_metadata_import.xml Wed Aug 07 12:54:19 2024 +0000 @@ -0,0 +1,147 @@ +<tool id="omero_metadata_import" name="OMERO Metadata 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@">0</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> + <requirement type="package" version="21.0.2">openjdk</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + python $__tool_directory__/omero_metadata_upload.py + --user $__user__.extra_preferences.get('omero|username', $test_username) + --pws $__user__.extra_preferences.get('omero|password', $test_password) + --host $omero_host + --port $omero_port + --obj_type $obj_type + --ann_type $ann_type + --ann_file $ann_file + --an_name $an_name + --log_file $log + #if $object_id_selection == "existing_object" + --did "$did" + #end if + ]]></command> + <inputs> + <param argument="omero_host" type="text" optional="false" label="OMERO host URL"/> + <param argument="omero_port" type="integer" optional="false" value="4064" label="OMERO port"/> + <param argument="obj_type" type="select" optional="true" label="Target Object Type"> + <option value="project">Project</option> + <option value="screen">Screen</option> + <option value="dataset">Dataset</option> + <option value="image">Image</option> + </param> + <conditional name="object_id"> + <param name="object_id_selection" type="select" label="Selection" help="Create a new OMERO object or target an existing one"> + <option value="new_object">Create new object</option> + <option value="existing_object">Target an existing object</option> + </param> + <when value="new_object"/> + <when value="existing_object"> + <param name="did" type="integer" value="" optional="false" label="Object ID"/> + </when> + </conditional> + <param argument="ann_type" type="select" optional="false" label="Annotation type" help="Select annotation format"> + <option value="table">Table</option> + <option value="KV">Key-Value Pairs</option> + </param> + <param argument="ann_file" type="data" format="tabular" optional="false" label="Annotation file" help="Select annotation file"/> + <param argument="an_name" type="text" optional="false" label="Annotation Name"/> + <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="obj_type" value="project"/> + <param name="ann_type" value="table"/> + <param name="object_id_selection" value="new_object"/> + <param name="ann_file" value="metadata.tsv"/> + <param name="an_name" value="Table_Test"/> + <param name="test_username" value="root"/> + <param name="test_password" value="omero"/> + <output name="log" value="output_table_import.txt" ftype="txt"> + <assert_contents> + <has_text text="SUCCESS: Successfully uploaded metadata for project"/> + </assert_contents> + </output> + </test> + <test> + <param name="omero_host" value="host.docker.internal"/> + <param name="omero_port" value="6064"/> + <param name="obj_type" value="dataset"/> + <param name="ann_type" value="KV"/> + <param name="object_id_selection" value="new_object"/> + <param name="ann_file" value="metadata.tsv"/> + <param name="an_name" value="KV_Test"/> + <param name="test_username" value="root"/> + <param name="test_password" value="omero"/> + <output name="log" value="output_KV_import.txt" ftype="txt"> + <assert_contents> + <has_text text="SUCCESS: Successfully uploaded metadata for dataset"/> + </assert_contents> + </output> + </test> + <test> + <param name="omero_host" value="host.docker.internal"/> + <param name="omero_port" value="6064"/> + <param name="obj_type" value="dataset"/> + <param name="ann_type" value="KV"/> + <param name="object_id_selection" value="existing_object"/> + <param name="did" value="1"/> + <param name="ann_file" value="metadata.tsv"/> + <param name="an_name" value="Additional_KV_Values"/> + <param name="test_username" value="root"/> + <param name="test_password" value="omero"/> + <output name="log" value="output_target_import.txt" ftype="txt"> + <assert_contents> + <has_text text="SUCCESS: Successfully uploaded metadata for dataset"/> + </assert_contents> + </output> + </test> + </tests> + <help> +Description +----------- + +Tool to import metadata (Table and K/V pairs) into user defined OMERO.server. +Metadata can be attached to an existing OMERO object (Project, Dataset, Screen, or Image). +Optionally, a new OMERO object can be created before uploading the metadata. +If the object does not exist, a new one will be created. + +**Tabular metadata file example** + +- Table + + +------------+---------------+---------------+ + | image_id | attribute_1 | attribute_2 | + +============+===============+===============+ + | 235 | 0 | 1 | + +------------+---------------+---------------+ + | 564 | 1 | 1 | + +------------+---------------+---------------+ + | 120 | 0 | 1 | + +------------+---------------+---------------+ + +- Key-Value Pairs + + +--------+---------+----------+ + | Key1 | Key2 | Key3 | + +========+=========+==========+ + | Value1 | Value2 | Value3 | + +--------+---------+----------+ + </help> + <citations> + <citation type="doi">10.1038/nmeth.1896</citation> + </citations> +</tool>