add WebAtlas pipeline 0.5.3 by dannyspadaro · Pull Request #1794 · bgruening/galaxytools

dannyspadaro · 2026-03-03T12:41:23Z

FOR CONTRIBUTOR:

I have read the CONTRIBUTING.md document and this tool is appropriate for the tools-iuc repo.
License permits unrestricted use (educational + commercial)
This PR adds a new tool or tool collection
This PR updates an existing tool or tool collection
This PR does something else (explain below)

There are two labels that allow to ignore specific (false positive) tool linter errors:

skip-version-check: Use it if only a subset of the tools has been updated in a suite.
skip-url-check: Use it if github CI sees 403 errors, but the URLs work.

dannyspadaro · 2026-03-03T12:54:01Z

I have 2 docker containers containing the dependencies and python scripts of webatlas (1 container specifically for build_config and 1 container for all other tools). Where should I put/upload them?

…_config.xml accordingly

…rkflow

…texts, added tool descriptions, added/fixed tests

…ry zipping for efficiency, adjusted tests

nilchia · 2026-04-07T09:16:14Z

Hi, please add a .shed.yml file here. You can find examples in other tools in this repo.

pavanvidem

I will review the remaining tools later.

Co-authored-by: Pavankumar Videm <pavanvidem@gmail.com>

nilchia

Great work! @dannyspadaro

nilchia · 2026-04-07T11:27:51Z

+        <import>macros.xml</import>
+    </macros>
+    <requirements>
+        <container type="docker">dannyspadaro/webatlas-pipeline-build-config:0.5.3-galaxy</container>


Is there a link to the DockerFile?
Maybe you can add a comment to the repo.

Currently you can find the Dockerfile here: https://github.com/dannyspadaro/webatlas-pipeline/tree/update_dependencies
You can build it by running /envs/build-docker-imgs.sh
I will replace the container once PR usegalaxy-eu/docker-webatlas#1 is done

nilchia · 2026-04-08T09:02:42Z

+                <option value="spaceranger">SpaceRanger output archive (ZIP)</option>
+                <option value="xenium">Xenium output archive (ZIP)</option>
+                <option value="merscope">MERSCOPE output archive (ZIP)</option>


ZIP files will be error-prone and will fail if an specific input is not in the ZIP.

Alternatively, Maybe you can use and SpatialData object (output of spatialdata_io tool) which is already a ZARR file and extract the AnnData ZARR from it?

Would users necessarily (want to) run spatialdata_io beforehand?
Trying/implementing this now would complicate the work on my thesis a lot I think, so I'd like to postpone it if that's okay.

nilchia · 2026-04-08T10:14:05Z

+                <option value="spaceranger">SpaceRanger output archive (ZIP)</option>
+                <option value="xenium">Xenium output archive (ZIP)</option>
+                <option value="merscope">MERSCOPE output archive (ZIP)</option>
+                <!-- Currently there is no usecase for this option. It can be implemented on request -->


ZIP files will be error-prone and will fail if an specific input is not in the ZIP.

Alternatively, Maybe you can use and SpatialData object (output of spatialdata_io tool) which is already a ZARR file and extract the AnnData ZARR from it?

same for generate_image.xml

nilchia · 2026-04-08T10:17:29Z

+        <param name="input_label_img" type="data" format="tif,tiff" optional="true" label="Label image TIFF" help="Optional label TIFF image to include in the SpatialData Zarr."/>
+    </inputs>
+    <outputs>
+        <data name="output_zarr" format="zarr.zip" label="${tool.name} on ${on_string}: ZIP-compressed SpatialData Zarr output"/>


Suggested change

<data name="output_zarr" format="zarr.zip" label="${tool.name} on ${on_string}: ZIP-compressed SpatialData Zarr output"/>

<data name="output_zarr" format="spatialdata.zip" label="${tool.name} on ${on_string}: ZIP-compressed SpatialData Zarr output"/>

The output of write_spatialdata.py is actually a Zarr, so this should also be Zarr I think?

nilchia · 2026-04-08T10:18:23Z

+        <param name="input_label_img" location="https://zenodo.org/records/19053876/files/visium-breast-cancer-label.tif"/>
+        <output name="output_zarr">
+            <assert_contents>
+                <has_archive_member path="visium-breast-cancer-spatialdata.zarr/.zgroup"/>


You can also assert the file contents. You can take a look at spatialdata too suite on tools IUC repo

nilchia · 2026-04-08T10:24:48Z

Hi @dannyspadaro, Thanks for the great work!

Two other points from my side:

Some parts can be replaced by spatialdata tool suite, for example, write_spatialdata.xml. You can also make the tool accept spatialdata.zip and then parse the info you need for webatlas from there.
If possible, please combine the different tools here into one. It looks like you have only one main tool, and the rest are for preparing the input for that tool.

One minor point: pleasae add "webatlas_" to the xml files here. please check the best practive here: https://galaxy-iuc-standards.readthedocs.io/en/latest/best_practices/tool_xml.html#tool-ids

nilchia · 2026-04-08T10:28:38Z

Please also run planemo l in your local tool directory to see other linting errors

…json_, fixed outputs

pavanvidem · 2026-04-09T14:21:33Z

+            <param name="stem" value="visium-breast-cancer"/>
+            <param name="image_type" value="label"/>
+            <output name="output_zarr">
+                <extra_files type="file" name="visium-breast-cancer-label.zarr/OME/METADATA.ome.xml" location="https://zenodo.org/records/19461849/files/consolidate_expected_ome_label_metadata_contains.txt" compare="contains"/>


I am not sure whether compare="contains" works for extra_files. Here anyways you want to check the file in the zarr is same as the file you provided. Please use compare="sim_size" with a small delta.

pavanvidem · 2026-04-09T14:22:29Z

+            <param name="stem" value="visium-breast-cancer"/>
+            <param name="image_type" value="raw"/>
+            <output name="output_zarr">
+                <extra_files type="file" name="visium-breast-cancer-raw.zarr/OME/METADATA.ome.xml" location="https://zenodo.org/records/19461849/files/consolidate_expected_ome_raw_metadata_contains.txt" compare="contains"/>


same as above, use compare="sim_size"

pavanvidem · 2026-04-09T15:14:54Z

+            </section>
+        </conditional>
+        <output name="output_zarr">
+            <extra_files type="file" name="h5ad-anndata.zarr/.zmetadata" location="https://zenodo.org/records/19461849/files/h5ad_var_subset_expected_zmetadata_contains.txt" compare="contains"/>


please replace the contains with sim_size. Also for all extra_files comparison in other tests too

…, add macros, fix citation, remove filters

Co-authored-by: Pavankumar Videm <pavanvidem@gmail.com>

bgruening · 2026-05-04T09:39:50Z

Tests are not running, the shed.yml file is missing.

pavanvidem · 2026-05-04T09:59:25Z

Added shed.yml. The tests still might fail because there is no required Docker container. Please review it here: usegalaxy-eu/docker-webatlas#2

bgruening · 2026-05-04T11:58:29Z

Commented, in the Docker one. You need to create a tagged release to get a new contianer.

bgruening · 2026-05-04T21:44:16Z

+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+        if tiffinfo $input_image | grep "Compression Scheme:" | grep -wq "JPEG";


single quotes

bgruening · 2026-05-04T21:45:27Z

+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+        if tiffinfo $input_image | grep "Compression Scheme:" | grep -wq "JPEG";


What is this doing? Can we not make decisions based on Galaxy metadata of those datasets?

checks if it is a JPEG compressed TIFF image. I don't think this information is stored in the metadata.

Co-authored-by: Björn Grüning <bjoern@gruenings.eu>

add WebAtlas

13a2601

dannyspadaro added 14 commits March 4, 2026 18:23

fixed resolution parameter

8233bb9

added vitessce_options to build_config

b71249c

fixed mappings handling in build_config to allow false values

35c66af

added modified build_config.py that works with galaxy. adjusted build…

108d647

…_config.xml accordingly

reordered parameter attributes to comply with iuc standards

fd3266c

fixed tests and adjusted build_config params to function better in wo…

0cd5c0e

…rkflow

added zenodo links for test-data

aa1e49c

Add write_spatialdata.xml, switch to updated docker containers

901a369

Restructured all tools, added sanitizers, added/fixed parameter help …

1540d6d

…texts, added tool descriptions, added/fixed tests

removed obsolete files

34b1925

fixed generate_image tests

bc2d3fe

added proper filename for consolidate_md output

c3f2812

Replaced conditionals in vitessce_options with sections for workflows

27fa161

changed outputs of router + consolidate_md to zarr, removed unnecessa…

a134f3e

…ry zipping for efficiency, adjusted tests

pavanvidem reviewed Apr 7, 2026

View reviewed changes

dannyspadaro and others added 3 commits April 7, 2026 20:20

Apply suggestions from code review

2498267

Co-authored-by: Pavankumar Videm <pavanvidem@gmail.com>

added macros for sanitizers, changed asserts in build_config.xml

7e1bc4a

added missing zenodo links to tests

40b4e92

nilchia reviewed Apr 8, 2026

View reviewed changes

dannyspadaro added 2 commits April 8, 2026 18:50

fixed if statements, removed default parameters in tests and use has_…

6796c5a

…json_, fixed outputs

changed vitessce options dimension help texts

e6558fa

pavanvidem reviewed Apr 9, 2026

View reviewed changes

dannyspadaro and others added 3 commits April 12, 2026 18:12

fix custom_layout, add build_config help text, remove /usr/local/bin/…

abb8456

…, add macros, fix citation, remove filters

Apply suggestions from code review

3ed298f

Co-authored-by: Pavankumar Videm <pavanvidem@gmail.com>

added tool help sections

6cdd180

pavanvidem added 4 commits April 28, 2026 17:58

fix router.xml tests and add h5 asserts

27aabb8

typo in select

fd21dba

add asserts for consolidate_md

bab3e74

fix zarr path in consolidate test

8a22392

pavanvidem marked this pull request as ready for review April 30, 2026 12:30

add .shed.yml

dd1191c

pavanvidem added 2 commits May 4, 2026 23:26

update the container

f4fad45

update the zenodo record

1b962c7

bgruening reviewed May 4, 2026

View reviewed changes

pavanvidem and others added 2 commits May 4, 2026 23:49

Update tools/webatlas/build_config.xml

5f5d7f2

Co-authored-by: Björn Grüning <bjoern@gruenings.eu>

add single quotes

e514d8e

	<data name="output_zarr" format="zarr.zip" label="${tool.name} on ${on_string}: ZIP-compressed SpatialData Zarr output"/>
	<data name="output_zarr" format="spatialdata.zip" label="${tool.name} on ${on_string}: ZIP-compressed SpatialData Zarr output"/>

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dannyspadaro commented Mar 3, 2026

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nilchia commented Apr 7, 2026

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nilchia commented Apr 8, 2026

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bgruening commented May 4, 2026

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