Request for adding TopAnat tool to IUC: please review by fbastian · Pull Request #8218 · galaxyproject/tools-iuc

fbastian · 2026-07-24T12:31:13Z

FOR CONTRIBUTOR:

I have read the CONTRIBUTING.md document and this tool is appropriate for the tools-iuc repo.
Use of AI
- The contribution is mostly AI generated
- The contribution has been assisted by AI
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.

To request a review once your PR is ready, comment "please review" on the PR. This will
automatically apply the ready-for-review label if the PR is not a draft, all review
threads are resolved, and all CI checks have passed.

fbastian · 2026-07-24T12:31:28Z

Please review

tools-iuc · 2026-07-24T12:31:39Z

⏳ Some CI checks are still running. Please wait for them to complete before requesting a review.

…rgument handling directly into the XML config

fbastian · 2026-07-27T14:35:16Z

@bgruening Could you please add the skip-url-check label? It seems to be the cause of a check error, but apparently I can't modify labels.

…some environments

bgruening · 2026-07-27T18:59:03Z

Done.

fbastian · 2026-07-29T14:14:35Z

please review

bernt-matthias · 2026-08-01T10:13:11Z

+    The species for which the analysis is performed. Must be provided in the format ``Genus_species``
+    (e.g. ``Homo_sapiens``, ``Mus_musculus``, ``Danio_rerio``). See the `Bgee website`_ for the full
+    list of supported species.


Suggested change

The species for which the analysis is performed. Must be provided in the format ``Genus_species``

(e.g. ``Homo_sapiens``, ``Mus_musculus``, ``Danio_rerio``). See the `Bgee website`_ for the full

list of supported species.

The species for which the analysis is performed.

SaimMomin12

Thanks @fbastian for the PR. Some comments inline

SaimMomin12 · 2026-08-05T09:37:35Z

+- Statistics
+- Single Cell


Suggested change

- Statistics

- Single Cell

SaimMomin12 · 2026-08-05T09:38:00Z

@@ -0,0 +1,456 @@
+<tool id="topanat" name="TopAnat" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0">


Suggested change

<tool id="topanat" name="TopAnat" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0">

<tool id="topanat" name="TopAnat" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">

Bump profile to 25.0

SaimMomin12 · 2026-08-05T09:38:23Z

+    <description>GO-like enrichment of anatomical terms and cell types mapped to genes by expression patterns</description>
+    <macros>
+        <token name="@TOOL_VERSION@">2.38.1</token>
+        <token name="@VERSION_SUFFIX@">0</token>


Suggested change

<token name="@VERSION_SUFFIX@">0</token>

<token name="@VERSION_SUFFIX@">0</token>

<token name="@PROFILE@">25.0</token>

SaimMomin12 · 2026-08-05T09:38:53Z

+cat(paste("Time taken:", time_taken, "seconds\n"))
+        ]]></configfile>
+    </configfiles>
+    <inputs>


Can we do planemo format topanat.xml?

SaimMomin12 · 2026-08-05T09:39:39Z

+                <param name="fg_file"
+                    argument="--fgFile"
+                    type="data"
+                    format="tabular,txt"


Suggested change

format="tabular,txt"

format="tabular"

The lint job resolved the PR via an associated-PR lookup (sharesight/find-github-pull-request, then 8BitJonny/gh-get-current-pr). That endpoint omits open PRs whose head commit is reachable from the queried repo's default branch, and the action queries the fork rather than the base repo on pull_request events. Two of the 25 open PRs sampled hit this today (galaxyproject#8279, galaxyproject#8218) and both carry skip labels: the step was gated off, EXTRA_SKIP was never written, and planemo linted URLs anyway with no indication the label had been ignored. On pull_request the PR number is in the event payload, so query it directly. This drops the third-party action from the fork-facing path entirely and restores exact label matching over a JSON array, which a label containing a comma could previously spoof. The labels are fetched at run time rather than read from the payload, so applying a label after a failed run and re-running now works; pull_request does not fire on 'labeled', so payload labels would be stale on re-run. Direct pushes to the default branch skip the step and lint with full checks, replacing the failIfNotFound abort. Also add explicit least-privilege permissions to both jobs, and fall back to github.token in deploy-report: an explicitly empty token overrides create-or-update-comment's own github.token default, so repos without secrets.PAT failed there. Refs: bgruening/galaxytools#1944

fbastian and others added 10 commits April 29, 2026 11:58

Initialization for TopAnat tool

320014a

Add R script to be able to parameterize calls to BgeeDB R package

f412f80

Initial version topaant.xml

5e758da

Add test cases

458ab02

Add shed yaml file

cf0f067

Misc improvements

f013e26

Fix planemo warnings

976a0db

Add stage options, and tests

585a6e0

Explicit Ensembl versions used

fd4adf4

Merge branch 'galaxyproject:main' into main

2af6f6d

github-project-automation Bot added this to Galaxy Tool Developers SIG Board Jul 24, 2026

github-project-automation Bot moved this to Triage/Discuss in Galaxy Tool Developers SIG Board Jul 24, 2026

fbastian marked this pull request as draft July 24, 2026 12:56

bgruening reviewed Jul 26, 2026

View reviewed changes

Comment thread tools/topanat/topanat.xml

Comment thread tools/topanat/topanat.R Outdated

fbastian added 2 commits July 27, 2026 15:43

Add required file in XML

5ca8498

Implement recommendation from bgruening to include the R script for a…

b0593ce

…rgument handling directly into the XML config

Implements copilot suggestion about locale that could cause error in …

4b20843

…some environments

bgruening added the skip-url-check Allow IUC members to skip the URL linter in PR reviews. label Jul 27, 2026

SaimMomin12 closed this Jul 28, 2026

github-project-automation Bot moved this from Triage/Discuss to Blocked / Not Planned in Galaxy Tool Developers SIG Board Jul 28, 2026

SaimMomin12 reopened this Jul 28, 2026

github-project-automation Bot moved this from Blocked / Not Planned to In progress in Galaxy Tool Developers SIG Board Jul 28, 2026

fbastian and others added 3 commits July 29, 2026 16:03

Merge branch 'galaxyproject:main' into main

76d5ea0

Fix problem of package NAMESPACE

e895211

Fix problem of 'none' returned when no data type selected

5d699af

fbastian marked this pull request as ready for review July 29, 2026 14:14

tools-iuc Bot added the ready-for-review label Jul 29, 2026

tools-iuc Bot moved this from In progress to Needs Review in Galaxy Tool Developers SIG Board Jul 29, 2026

bernt-matthias reviewed Aug 1, 2026

View reviewed changes

SaimMomin12 reviewed Aug 5, 2026

View reviewed changes

Navigation Menu

Uh oh!

Request for adding TopAnat tool to IUC: please review - #8218

Request for adding TopAnat tool to IUC: please review#8218
fbastian wants to merge 16 commits into
galaxyproject:mainfrom
BgeeDB:main

fbastian commented Jul 24, 2026

Uh oh!

fbastian commented Jul 24, 2026

Uh oh!

tools-iuc Bot commented Jul 24, 2026

Uh oh!

Uh oh!

Uh oh!

fbastian commented Jul 27, 2026 •

edited

Loading

Uh oh!

bgruening commented Jul 27, 2026

Uh oh!

fbastian commented Jul 29, 2026

Uh oh!

bernt-matthias Aug 1, 2026

Uh oh!

SaimMomin12 left a comment

Uh oh!

SaimMomin12 Aug 5, 2026

Uh oh!

SaimMomin12 Aug 5, 2026

Uh oh!

SaimMomin12 Aug 5, 2026

Uh oh!

SaimMomin12 Aug 5, 2026

Uh oh!

SaimMomin12 Aug 5, 2026

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

4 participants

		@@ -0,0 +1,456 @@
		<tool id="topanat" name="TopAnat" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0">

	<token name="@VERSION_SUFFIX@">0</token>
	<token name="@VERSION_SUFFIX@">0</token>
	<token name="@PROFILE@">25.0</token>

Uh oh!

Conversation

fbastian commented Jul 24, 2026

Uh oh!

fbastian commented Jul 24, 2026

Uh oh!

tools-iuc Bot commented Jul 24, 2026

Uh oh!

Uh oh!

Uh oh!

fbastian commented Jul 27, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Uh oh!

bgruening commented Jul 27, 2026

Uh oh!

fbastian commented Jul 29, 2026

Uh oh!

bernt-matthias Aug 1, 2026

Choose a reason for hiding this comment

Uh oh!

SaimMomin12 left a comment

Choose a reason for hiding this comment

Uh oh!

SaimMomin12 Aug 5, 2026

Choose a reason for hiding this comment

Uh oh!

SaimMomin12 Aug 5, 2026

Choose a reason for hiding this comment

Uh oh!

SaimMomin12 Aug 5, 2026

Choose a reason for hiding this comment

Uh oh!

SaimMomin12 Aug 5, 2026

Choose a reason for hiding this comment

Uh oh!

SaimMomin12 Aug 5, 2026

Choose a reason for hiding this comment

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

4 participants

fbastian commented Jul 27, 2026 •

edited

Loading