Wrap Liana toolkit for Single-cell and Spatial Transcriptomics #7625

khaled196 · 2026-01-26T15:23:26Z

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)

Co-authored-by: Ona <[email protected]>

SaimMomin12

Some preliminary comments inline. @nilchia @pavanvidem would you like to review this PR more in detail?

tools/liana/macros.xml

Co-authored-by: Saim Momin <[email protected]>

khaled196 · 2026-01-28T10:27:20Z

I am changing the parameters label and help section. The updates will be shared ASAP

bernt-matthias · 2026-01-28T10:28:01Z

tools/liana/misty.xml

+            <section name="advanced_common">
+                <param name="show_log" value="true"/>
+            </section>
+            <output name="misty_out" location="https://zenodo.org/records/18388645/files/genericMistyData_rf.h5mu" ftype="h5mu" compare="sim_size" delta="100000">


Pleas add a has_size assertion instead of sim_size. This has the huge advantage that we do not need to save the test data anywhere.

Also note that there are has_h5_... assertions that could be useful here, e.g. https://docs.galaxyproject.org/en/master/dev/schema.html#has-h5-attribute

Hi @bernt-matthias

The tools hate the has_size when they were tested on GitHub,

<has_size size="1500000" delta="100000"/> <has_h5_keys keys="uns/liana_res"/>

For some of the tests, I am using both of the assertions, butthey still fail

They are equivalent to using compare="sim_size" where the size is determined for the given file.

tools/liana/misty.xml

Co-authored-by: Ona <[email protected]>

bernt-matthias · 2026-01-29T18:18:12Z

tools/liana/multi.xml

+            <section name="advanced_common">
+                <param name="show_log" value="true"/>
+            </section>
+            <output name="mdata_out" location="https://zenodo.org/records/18388645/files/multi_lrs_to_views.h5mu" ftype="h5mu">


Suggested change

<output name="mdata_out" location="https://zenodo.org/records/18388645/files/multi_lrs_to_views.h5mu" ftype="h5mu">

<output name="mdata_out" ftype="h5mu">

Otherwise the file at zenodo and the file genereated in the test will be compared bitwise using diff which will fail:

Output misty_out: different than expected, difference (using diff): ( /tmp/tmp3dobkgt8genericMistyData_rf.h5mu v. /tmp/tmp4ebi8nslgenericMistyData_rf.h5mu ) Binary data detected, not displaying diff

@bernt-matthias

Thank you, I have updated the wrapper with this. The tools fail due to a Zenodo issue, not for the test itself. I might move the input files to the GitHub repo and keep the output in Zenodo.

But please let me know if I need to update the wrapper to comply with Galaxy.

I have seen Parameter 'adata': the previously selected dataset has entered an unusable state in other tools. So this is not a problem of your PR.

khaled196 · 2026-02-02T12:14:50Z

Hi @pavanvidem

Please check if the wrapper is ready, including the label and the help sections for the parameters.

pavanvidem · 2026-02-02T20:15:43Z

Hi @pavanvidem

Please check if the wrapper is ready, including the label and the help sections for the parameters.

@khaled196 where did you find the labels and help text? It seems they are far off from the documentation here: https://liana-py.readthedocs.io/en/latest/api.html

tools/liana/macros.xml

pavanvidem · 2026-02-02T18:34:11Z

tools/liana/macros.xml

+    </xml>
+    <xml name="bio_tools">
+        <xrefs>
+            <xref type="bio.tools">liana</xref>


Can you please improve the bio.tools entry with links, description, edam topics and so on?

would adding xrf do that work?

Please go to https://bio.tools/liana, request edit access and update it.
Once the bio.tools entry is complete, you don't have to change anything in the Galaxy tool.

Please let me know if you require any assistance.

tools/liana/macros.xml

pavanvidem · 2026-02-02T20:11:32Z

tools/liana/macros.xml

+    </xml>
+    <xml name="param_kernel">
+        <param argument="kernel" type="select" label="Spatial weight kernel" help="Kernel for computing spatial weights from distance. misty_rbf: Gaussian-like (default); gaussian: standard Gaussian; exponential: exponential decay; linear: inverse distance weighting.">
+            <option value="misty_rbf" selected="true">misty_rbf - MISTy RBF (default)</option>


the default is not always misty_rbf. For example, in util.spatial_neighbors, gaussian is default. Please check again and use the correct default based on the function it is used in.

You can pass any attribute (for eg, value or help or selected of any param) by using a placeholder and pass the value while expanding macro.
Check out an example here:

A macro with placeholder: https://github.com/galaxyproject/tools-iuc/blob/main/tools/scanpy/macros.xml#L723-L725

expand the macro by passing a value: https://github.com/galaxyproject/tools-iuc/blob/main/tools/scanpy/normalize.xml#L133

pavanvidem · 2026-02-02T20:12:10Z

tools/liana/utils.xml

+                </param>
+                <param argument="max_neighbours" type="integer" value="100" min="1" label="Maximum neighbors" help="Maximum nearest neighbors to include per spot/cell. Default: 100. Limits computation.">
+                </param>
+                <expand macro="param_kernel"/>


the default is gaussian

pavanvidem · 2026-02-02T21:02:35Z

tools/liana/macros.xml

+    </xml>
+    <!-- Simple resource name parameter -->
+    <xml name="param_resource_name">
+        <param argument="resource_name" type="select" label="Ligand-receptor database" help="Built-in database of ligand-receptor pair annotations. consensus: combines multiple resources (recommended); mouseconsensus: for mouse data. Affects which interactions are considered.">


Is the DB fetched every time one of the ligand-receptor methods is called?
If the DBs are updated, it might break the reproducibility. In that case, we need a datamanager that caches all the resources on Galaxy.

Yes, the DB was obtained from Liana. I can see your concern if anyupdate happend. Any resources to create DM?

Check this out: https://galaxyproject.org/admin/tools/data-managers/

There are links at the bottom of the page.

pavanvidem · 2026-02-02T21:07:31Z

tools/liana/macros.xml

+                <option value="interactions">Enter specific interaction pairs</option>
+            </param>
+            <when value="resource_name">
+                <param argument="resource_name" type="select" label="Ligand-receptor database" help="Built-in L-R pair database. consensus recommended for general use; choose species-specific versions for cross-species studies.">


Same as before. If it breaks reproducibilty, we might need a datamanager.

pavanvidem · 2026-02-02T21:19:04Z

tools/liana/resource.xml

@@ -0,0 +1,254 @@
+<tool id="liana_resource" name="Liana Resource" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">


For all the LR-methods in single-cell.xml, there is a select parameter that allows the user to select the resource.
So, why and where should the user run this tool?

https://liana-py.readthedocs.io/en/latest/notebooks/mofatalk.html

the tools here added because of this tutorial.

I just saw that it is also used in some other tutorials. Some functions need db_path param, which is an SQL DB, if not provided, it downloads from somewhere. It again breaks reproducibility.

As we discussed earlier, let's focus on the functions that are required for the first and last tutorials.

@nilchia any other tutorials of interest?

If some function downloads the data on the fly and is not used in the tutorials of interest, then we can safely leave them out now.

pavanvidem · 2026-02-02T21:26:42Z

tools/liana/macros.xml

+        <param argument="seed" type="integer" value="1337" label="Random seed" help="Seed for reproducibility in stochastic methods. Default: 1337."/>
+    </xml>
+    <xml name="param_verbose">
+        <param argument="verbose" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Verbose progress output" help="If enabled: print progress messages during computation."/>


If percentage-wise progress printed to stdout, it might generate a huge stdout. Please remove this param entirely and use the default of False in the function call.

pavanvidem · 2026-02-02T21:40:02Z

tools/liana/macros.xml

+        </param>
+    </xml>
+    <xml name="param_de_method">
+        <param argument="de_method" type="select" label="Differential expression test" help="Statistical method for rank_genes_groups (1-vs-Rest). t-test: parametric; wilcoxon: non-parametric, robust; logreg: logistic regression. Default: t-test.">


Good find. Is a list of possible DE methods documented somewhere?

https://scanpy.readthedocs.io/en/stable/generated/scanpy.tl.rank_genes_groups.html#:~:text=to%20all%20genes.-,method,wilcoxon%27%2C%20%27t%2Dtest_overestim_var%27%5D%20%7C%20None%20(default%3A%20None),-The%20default%20method

I think in the scanpy documentation, I am not sure about the rest; it was very annoying to get those parameters

pavanvidem · 2026-02-02T21:42:31Z

Halfway through. I will review the rest soon.

pavanvidem · 2026-02-03T10:11:09Z

@khaled196, there are some unused macros or macros used only once. It will be hard to maintain if there are nested macros that are used only once in the entire suite. For example, the macros used in spatial.xml can be removed because most of the parameters are only used once in the tool suite. Please create (nested) macros only when required.

khaled196 · 2026-02-03T19:40:23Z

Hi @pavanvidem
Please check if the wrapper is ready, including the label and the help sections for the parameters.

@khaled196, where did you find the labels and help text? It seems they are far off from the documentation here: https://liana-py.readthedocs.io/en/latest/api.html

The help section and labels are my best attempts to clarify the parameters, as they can sometimes be unclear. Using the parameters provided by the API can be misleading for users.

I went through them again to read and adjust them

khaled196 and others added 7 commits January 22, 2026 13:54

create liana

2204b32

Co-authored-by: Ona <[email protected]>

add liana tools

d5ac7d0

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update misty

dca58dc

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add liana toolkit

810fecd

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fix linit

b1347e6

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remove tests to zenodo

c3eaf91

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fix tests

f794b37

SaimMomin12 reviewed Jan 28, 2026

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khaled196 changed the title ~~Wrapp Liana toolkit for Single-cell and Spatial Transcriptomics~~ Wrap Liana toolkit for Single-cell and Spatial Transcriptomics Jan 28, 2026

bernt-matthias reviewed Jan 28, 2026

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khaled196 and others added 6 commits January 28, 2026 12:24

update tests and remove redundunt info

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fix linting

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upfate help

9f34ed1

Merge remote-tracking branch 'refs/remotes/origin/Liana' into Liana

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update labels and help, fix macros

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update test files and spatial

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bernt-matthias reviewed Jan 29, 2026

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remove zenodo location from failled tests

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khaled196 requested a review from bernt-matthias February 2, 2026 11:07

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khaled196 added 3 commits February 3, 2026 13:46

update tools

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update the tool

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update parameters labels and help

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	<output name="mdata_out" location="https://zenodo.org/records/18388645/files/multi_lrs_to_views.h5mu" ftype="h5mu">
	<output name="mdata_out" ftype="h5mu">

		@@ -0,0 +1,254 @@
		<tool id="liana_resource" name="Liana Resource" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">

Wrap Liana toolkit for Single-cell and Spatial Transcriptomics #7625

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Wrap Liana toolkit for Single-cell and Spatial Transcriptomics #7625

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