Galaxy Workflow - ARC2OMERO Version 1
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This Galaxy 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.
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
Test Dataset
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| Deepth of the folder under "dataset" where the image are stored | Deepth of the folder under "dataset" where the image are stored | n/a |
|
| Image File Extension | Image File Extension | Image format of the image to import into OMERO |
|
| Input ARC .zip file | Input ARC .zip file | Input here the .zip file from the ARC repository. |
|
| OMERO server URL | OMERO server URL | n/a |
|
Steps
| ID | Name | Description |
|---|---|---|
| 4 | Unzip | toolshed.g2.bx.psu.edu/repos/imgteam/unzip/unzip/6.0+galaxy2 |
| 5 | Excel to Tabular | Extract the metadata from the assay toolshed.g2.bx.psu.edu/repos/ufz/xlsx2tsv/xlsx2tsv/0.1.0+galaxy0 |
| 6 | Select | Grep1 |
| 7 | Filter Tabular | toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular/3.3.1 |
| 8 | Cut | Cut1 |
| 9 | Transpose | toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose/1.9+galaxy0 |
| 10 | Text reformatting | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.5+galaxy3 |
| 11 | Column Regex Find And Replace | toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.3 |
| 12 | Parse parameter value | param_value_from_file |
| 13 | Parse parameter value | param_value_from_file |
| 14 | Unzip | toolshed.g2.bx.psu.edu/repos/imgteam/unzip/unzip/6.0+galaxy2 |
| 15 | OMERO Image Import | toolshed.g2.bx.psu.edu/repos/ufz/omero_import/omero_import/5.18.0+galaxy6 |
| 16 | JQ | toolshed.g2.bx.psu.edu/repos/iuc/jq/jq/1.0 |
| 17 | Parse parameter value | param_value_from_file |
| 18 | OMERO Metadata Import | toolshed.g2.bx.psu.edu/repos/ufz/omero_metadata_import/omero_metadata_import/5.18.0+galaxy7 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| log | log | n/a |
|
Version History
Version 1 (earliest) Created 23rd Mar 2026 at 12:58 by Riccardo Massei
Initial commit
Open
master7a352b4
Creators and Submitter
Views: 358 Downloads: 44 Runs: 1
Created: 23rd Mar 2026 at 12:58
Last updated: 23rd Mar 2026 at 12:59
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