Galaxy Workflow to transferring ZIP ARC to OMERO

[rmassei]

Dear All,
I recently developed a Galaxy workflow for transferring a ARC to OMERO automatically. The workflow allows transferring ARC imaging data stored as .ZIP file to a target OMERO instance by 1) keeping the ARC structure and 2) automatize the metadata annotation of the assay.

Workflow is shared on the WorkfloHub at this link:
https://workflowhub.eu/workflows/2116

How does it works

The workflow extract all the ./assays/experiment/dataset/ file path and create an OMERO dataset containing the images. The "isa.assay.xlsx" file is used to add key-value pairs to the dataset.
Workflow Inputs

The workflow as three different data inputs:

• ARC .ZIP file: A zip file with the whole ARC. Can be downloaded from the DataPLANT ARC repo
• Image File Extension: Image formats (e.g. TIFF, PNG, JPEG) to upload into OMERO
• Target OMERO instance: OMERO instance where to upload the data
• Depth of the ARC dataset folder: How depth after ./assays/experiment/dataset/ images are stored. As example if images are assays/CLSM-stacks_oryzalin/dataset/treated the depth need to be set to 1. If assays/CLSM-stacks_oryzalin/dataset the depth need to be set to 0

At the present, it allows just to upload images stored in the assay/dataset folder and add metadata as key-value pairs collected from the isa.assay.xlsx file.

This draft workflow was just tested with just one ARC (given in the workflow description) and it relies a bit on my limited knowledge of ARC the structure. Furthermore, the workflow relies a bit of the standardized structure of the ARC, basically uploading files into OMERO according to predefined paths.

Any feedback to further develop it is welcome, I also guess that the workflow can be maybe simplify in some steps. I would like also to know if anybody can suggested me which kind of info in an ARC might be useful to be added in OMERO. What can be translated in a Tag and which can be the best structure to reconstruct in OMERO?