Mercurial > repos > ufz > omero_get_id
diff omero_get_id.xml @ 0:c23735b45a4a draft
planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 19d84fd5a372f1428e3e5670144881a56e8af8b2
| author | ufz |
|---|---|
| date | Tue, 22 Oct 2024 11:53:30 +0000 |
| parents | |
| children | ae07ea142e0f |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/omero_get_id.xml Tue Oct 22 11:53:30 2024 +0000 @@ -0,0 +1,178 @@ +<tool id="omero_get_id" name="OMERO get IDs" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT"> + <description> with ezomero </description> + <macros> + <import>macros.xml</import> + <token name="@VERSION_SUFFIX@">0</token> + </macros> + <xrefs> + <xref type="bio.tools">omero</xref> + </xrefs> + <expand macro="ezomero_requirements"/> + <command detect_errors="exit_code"><![CDATA[ + python '$__tool_directory__'/omero_get_id.py + --credential-file '$credentials' + @HOST_PORT@ + --final_obj_type '$cond_obj_type.final_obj_type' + --parent_obj_type '$cond_obj_type.parent_obj_type' + --parent_id $cond_obj_type.parent_id + --tsv_file '$tsv' + ]]></command> + <configfiles> + <expand macro="credentials"/> + </configfiles> + <inputs> + <expand macro="host_port"/> + <conditional name="cond_obj_type"> + <param argument="final_obj_type" type="select" optional="false" label="Type of object to fetch ID:"> + <option value="Project">All Project IDs</option> + <option value="Dataset">Dataset IDs</option> + <option value="Image">Image IDs</option> + <option value="Annotation">Annotation IDs (key values)</option> + <option value="Tag">Tag IDs</option> + <option value="Roi">ROI IDs</option> + <option value="Table">Table IDs</option> + </param> + <when value="Project"> + <param name="parent_obj_type" type="hidden" value="All"/> + <param name="parent_id" type="hidden" value="0"/> + </when> + <when value="Dataset"> + <param name="parent_obj_type" type="select" label="Which datasets?"> + <option value="All">All datasets</option> + <option value="Project">Only datasets from a Project</option> + </param> + <param name="parent_id" type="integer" value="0" optional="false" label="ID of the project (leave 0 if you selected All)."/> + </when> + <when value="Image"> + <param name="parent_obj_type" type="select" label="Which images?"> + <option value="All">All images</option> + <option value="Project">Only images from a Project</option> + <option value="Dataset">Only images from a Dataset</option> + <option value="Plate">Only images from a Plate</option> + <option value="Well">Only images from a Well</option> + </param> + <param name="parent_id" type="integer" value="0" optional="false" label="ID of the parent object above (leave 0 if you selected All)."/> + </when> + <when value="Annotation"> + <param name="parent_obj_type" type="select" label="Of which type of object?"> + <option value="Project">Annotations from a Project</option> + <option value="Dataset">Annotations from a Dataset</option> + <option value="Plate">Annotations from a Plate</option> + <option value="Well">Annotations from a Well</option> + <option value="Image">Annotations from an Image</option> + </param> + <param name="parent_id" type="integer" value="0" optional="false" label="ID of the object above."/> + </when> + <when value="Tag"> + <param name="parent_obj_type" type="select" label="Of which type of object?"> + <option value="Project">Tags from a Project</option> + <option value="Dataset">Tags from a Dataset</option> + <option value="Plate">Tags from a Plate</option> + <option value="Well">Tags from a Well</option> + <option value="Image">Tags from an Image</option> + </param> + <param name="parent_id" type="integer" value="0" optional="false" label="ID of the object above."/> + </when> + <when value="Roi"> + <param name="parent_obj_type" type="hidden" value="Image"/> + <param name="parent_id" type="integer" value="0" optional="false" label="ID of the image from which you want to get ROI IDs."/> + </when> + <when value="Table"> + <param name="parent_obj_type" type="select" label="Of which type of object?"> + <option value="Project">Table from a Project</option> + <option value="Dataset">Table from a Dataset</option> + <option value="Plate">Table from a Plate</option> + <option value="Well">Table from a Well</option> + <option value="Image">Table from an Image</option> + </param> + <param name="parent_id" type="integer" value="0" optional="false" label="ID of the object above."/> + </when> + </conditional> + </inputs> + <outputs> + <data name="tsv" format="tabular"/> + </outputs> + <tests> + <test> + <param name="omero_host" value="host.docker.internal"/> + <param name="omero_port" value="6064"/> + <conditional name="cond_obj_type"> + <param name="final_obj_type" value="Project"/> + </conditional> + <param name="test_username" value="root"/> + <param name="test_password" value="omero"/> + <output name="tsv" value="output_ids_project.tsv" ftype="tabular"> + <assert_contents> + <has_text text="1"/> + </assert_contents> + </output> + </test> + <test> + <param name="omero_host" value="host.docker.internal"/> + <param name="omero_port" value="6064"/> + <conditional name="cond_obj_type"> + <param name="final_obj_type" value="Dataset"/> + <param name="parent_obj_type" value="Project"/> + <param name="parent_id" value="1"/> + </conditional> + <param name="test_username" value="root"/> + <param name="test_password" value="omero"/> + <output name="tsv" value="output_ids_dataset.tsv" ftype="tabular"> + <assert_contents> + <has_text text="1"/> + </assert_contents> + </output> + </test> + <test> + <param name="omero_host" value="host.docker.internal"/> + <param name="omero_port" value="6064"/> + <conditional name="cond_obj_type"> + <param name="final_obj_type" value="Image"/> + <param name="parent_obj_type" value="Dataset"/> + <param name="parent_id" value="1"/> + </conditional> + <param name="test_username" value="root"/> + <param name="test_password" value="omero"/> + <output name="tsv" value="output_ids_image.tsv" ftype="tabular"> + <assert_contents> + <has_text text="1"/> + </assert_contents> + </output> + </test> + <test> + <param name="omero_host" value="host.docker.internal"/> + <param name="omero_port" value="6064"/> + <conditional name="cond_obj_type"> + <param name="final_obj_type" value="Tag"/> + <param name="parent_obj_type" value="Image"/> + <param name="parent_id" value="1"/> + </conditional> + <param name="test_username" value="root"/> + <param name="test_password" value="omero"/> + <output name="tsv" ftype="tabular"> + <assert_contents> + <has_text text="1"/> + </assert_contents> + </output> + </test> + </tests> + <help> +Description +----------- + +Tool to fetch project, dataset, images, annotations, tags, table and ROIs IDs user defined OMERO.server. + +Options: +Project -> Project IDs present in the OMERO.server +Dataset -> Dataset IDs present in a specific Project or in the server +Image -> Image IDs present in a specific Dataset or Project or Well or Plate or in the server +Annotation (Key-Value Pairs) -> Annotation IDs linked to an Image or Dataset or Project or Well or Plate +Tag -> Tag IDs linked to an Image or Dataset or Project or Well or Plate +ROI -> ROI IDs linked to an Image +Table -> Table linked to an Image or Dataset or Project or Well or Plate + + </help> + <citations> + <citation type="doi">10.1038/nmeth.1896</citation> + </citations> +</tool> \ No newline at end of file