Add Galaxy wrapper for LEMUR: Latent Embedding Multivariate Regression #7173

dianichj · 2025-07-25T15:37:25Z

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)

This PR adds a new Galaxy tool for the LEMUR R package, designed for fitting a latent embedding multivariate regression model to multi-condition single-cell data.

🧬 Tool purpose

LEMUR provides a parametric framework to:

Align multi-condition single-cell transcriptomics data
Predict log fold changes between conditions at single-cell resolution
Identify spatially coherent neighborhoods of cells with consistent transcriptional shifts
Perform pseudobulk differential expression testing on these neighborhoods

It is especially suited for complex experimental designs such as treatment vs. control, time-course, or disease progression studies.

📂 Tool contents

lemur.xml: Galaxy wrapper with required parameters and outputs
lemur.R: R script that runs the LEMUR pipeline (fit, align, test)
test-data/: Includes example RDS input and expected PDF/TSV outputs:
- UMAPs and volcano plots
- DE results and neighborhood summaries

🧪 Test data

The test data included are derived from a publicly available glioblastoma single-cell dataset. They demonstrate:

Successful model fitting
Harmony-based alignment
Visualization of DE results per condition

🛠️ Requirements

Conda packages required:

bioconductor-lemur
bioconductor-singlecellexperiment
r-optparse
r-tidyverse
r-uwot

These are defined in the wrapper's <requirements> section.

📌 Notes

Please help me improve this tool wrapper, it still needs work. Thanks so much for reviewing and for your help!

cc: @nilchia 🚀🖖

nilchia · 2025-07-25T15:43:02Z

Cool 🎉

nilchia

Super nice!!
Thanks @dianichj

tools/lemur/.gitignore

tools/lemur/lemur.xml

tools/lemur/lemur.R

tools/lemur/lemur.xml

nilchia · 2025-07-25T16:11:41Z

Please add a .shed.yml file.
https://github.com/dianichj/tools-iuc/blob/main/tools/seurat/.shed.yml

Co-authored-by: Amirhossein Nilchi <[email protected]>

…column param, updated R script, XML and test data (Zenodo links used, metadata.tsv local), added .shed.yml

tools/lemur/.shed.yml

nilchia · 2025-08-02T17:14:47Z

tools/lemur/lemur.R

@@ -9,10 +9,19 @@ suppressPackageStartupMessages({
  library(ggplot2)
 })

+#----- Function to save plots in different formats ----
+save_plot <- function(filename, plot, format = "pdf", width = 6, height = 5, dpi = 300) {


Please make the dpi, width, and height configurable.

tools/lemur/lemur.xml

nilchia · 2025-08-02T17:25:09Z

tools/lemur/lemur.xml

+    <param name="meta_table" type="data" format="tabular" label="Sample metadata table (TSV)" help="TSV file with one row per sample/cell. Must contain columns for condition and optionally for batch." />
+    <param name="condition_column" type="data_column" data_ref="meta_table" label="Condition column" help="Select the condition column (e.g., treatment vs control). Only appears after loading metadata." />
+    <param name="batch_column" type="data_column" data_ref="meta_table" optional="true" label="Batch column (optional)" help="Optional batch variable (e.g., patient ID). Only appears after loading metadata." />
+    <param name="contrast_condition" type="text" value="panobinostat" label="Condition for contrast (e.g. treatment)" />


I'm not sure if it is OK here to have a default value.
Maybe at least keep it as "treatment" please.

And please add validators for both text params.

ping for the validator

nilchia · 2025-08-02T17:26:43Z

tools/lemur/lemur.R

@@ -9,10 +9,19 @@ suppressPackageStartupMessages({
  library(ggplot2)
 })

+#----- Function to save plots in different formats ----
+save_plot <- function(filename, plot, format = "pdf", width = 6, height = 5, dpi = 300) {
+  ext <- tolower(format)


Your formats are already lowercase, no?

nilchia · 2025-08-02T17:28:47Z

tools/lemur/lemur.xml

-        <data name="gene_hist_pdf" format="pdf" from_work_dir="gene_hist.pdf" label="Gene histogram plot" />
-        <data name="chr_scatter_pdf" format="pdf" from_work_dir="chr_scatter.pdf" label="Chromosome scatter plot" />
-        <data name="tumor_umap_pdf" format="pdf" from_work_dir="tumor_umap.pdf" label="Tumor UMAP plot" />
+        <data name="gene_umap" format="pdf" from_work_dir="gene_umap.pdf" label="Gene UMAP plot">


Will this work? You are hardcoding it to look for gene_umap.pdf file.
Please add a test using other formats as output.

nilchia · 2025-08-02T17:29:29Z

tools/lemur/lemur.xml

+                <when input="plot_format" value="png" format="png"/>
+                <when input="plot_format" value="jpg" format="jpg"/>
+            </change_format>
+        </data>
        <data name="de_results" format="tabular" from_work_dir="de_results.tsv" label="LEMUR DE results" />


Please use this lable for all outputs:
${tool.name} on ${on_string}:

nilchia · 2025-08-02T17:32:23Z

tools/lemur/lemur.xml

+                <assert_contents>
+                    <has_line_matching expression="^name\tn_cells\t.*did_lfc$"/>
+                    <has_text text="ENSG00000210082"/>
+                </assert_contents>


Please also add has_n_lines so we know the file has correct number of genes

nilchia · 2025-08-02T17:34:45Z

tools/lemur/lemur.xml

+LEMUR uses the `SingleCellExperiment` (SCE) format because it is the standard Bioconductor structure for single-cell data in R. Unlike Seurat or AnnData, SCE is lightweight, interoperable, and not tied to a specific framework. It cleanly separates assays (e.g., expression values), cell metadata (`colData`), feature metadata (`rowData`), and reduced dimensions (`reducedDims`).
+
+For LEMUR to work correctly, the SCE object **must include**:
+- **`logcounts()`**: matrix of log-normalized gene expression.


It also needs counts

nilchia · 2025-08-02T17:39:11Z

Categories [['Statistical Analysis']] unknown.

tools/lemur/lemur.xml

Co-authored-by: Amirhossein Nilchi <[email protected]>

tools/lemur/lemur.xml

Co-authored-by: Amirhossein Nilchi <[email protected]>

… check, and DE testing

dianichj · 2025-08-06T15:53:44Z

Ping @nilchia :)!

tools/lemur/.shed.yml

Co-authored-by: Rand Zoabi <[email protected]>

bgruening · 2025-08-08T07:33:34Z

tools/lemur/lemur.xml

@@ -0,0 +1,271 @@
+<tool id="lemur" name="LEMUR" version="1.0.1+galaxy0" profile="25.0" license="MIT">


The version should be 1.4.0+galaxy0 I think to indicate the version for the main dependency.

For that you can use a macro

bgruening · 2025-08-08T07:34:23Z

tools/lemur/lemur.xml

+    <param name="meta_table" type="data" format="tabular" label="Sample metadata table (TSV)" help="TSV file with one row per sample/cell. Must contain columns for condition and optionally for batch." />
+    <param name="condition_column" type="data_column" data_ref="meta_table" label="Condition column" help="Select the condition column (e.g., treatment vs control). Only appears after loading metadata." />
+    <param name="batch_column" type="data_column" data_ref="meta_table" optional="true" label="Batch column (optional)" help="Optional batch variable (e.g., patient ID). Only appears after loading metadata." />
+    <param name="contrast_condition" type="text" value="panobinostat" label="Condition for contrast (e.g. treatment)" />


ping for the validator

bgruening · 2025-08-08T07:34:37Z

tools/lemur/lemur.xml

+    <param name="batch_column" type="data_column" data_ref="meta_table" optional="true" label="Batch column (optional)" help="Optional batch variable (e.g., patient ID). Only appears after loading metadata." />
+
+    <param name="contrast_condition" type="text" value="panobinostat" label="Condition for contrast (e.g. treatment)" />
+    <param name="reference_condition" type="text" value="ctrl" label="Reference condition (e.g. control)" />


a validator would be nice here as well

bgruening · 2025-08-08T07:35:18Z

tools/lemur/lemur.xml

+    <param name="tumor_annotation_column" type="text" value="chromosome"
+           label="Tumor annotation column in rowData"
+           help="Used for tumor classification. Default is 'chromosome'. Override if your SCE uses a different annotation column." />
+</inputs>


indentation is a bit off here, please use the galaxy-language-server to reformat this tool

bgruening · 2025-08-08T07:36:00Z

tools/lemur/lemur.xml

+           help="Used for tumor classification. Default is 'chromosome'. Override if your SCE uses a different annotation column." />
+</inputs>
+
+<outputs>


these are a lot of outputs, are all of them always needed? Should the user be able to select only a few of them?

bgruening · 2025-08-08T07:37:02Z

tools/lemur/lemur.xml

+  --output_umap 'umap.$plot_format'
+  --output_volcano 'volcano.$plot_format'
+  --output_de 'de_results.tsv'
+  #if str($sel_gene):


"#end if" is missing for some reason.

dianichj and others added 3 commits July 25, 2025 17:18

Add initial LEMUR tool wrapper, R script and test data

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Remove .RData and .Rhistory and add to .gitignore

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Merge branch 'galaxyproject:main' into lemur-wrapper1

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Merge branch 'galaxyproject:main' into lemur-wrapper1

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Merge branch 'galaxyproject:main' into lemur-wrapper1

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Update LEMUR tool: improved tumor annotation, added tumor_annotation_…

de02eb4

…column param, updated R script, XML and test data (Zenodo links used, metadata.tsv local), added .shed.yml

dianichj marked this pull request as ready for review August 1, 2025 14:58

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Refactor lemur wrapper and script: clean metadata handling, embedding…

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comment out test 2 and 3

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		@@ -0,0 +1,271 @@
		<tool id="lemur" name="LEMUR" version="1.0.1+galaxy0" profile="25.0" license="MIT">

Add Galaxy wrapper for LEMUR: Latent Embedding Multivariate Regression #7173

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Add Galaxy wrapper for LEMUR: Latent Embedding Multivariate Regression #7173

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dianichj commented Jul 25, 2025

🧬 Tool purpose

📂 Tool contents

🧪 Test data

🛠️ Requirements

📌 Notes

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nilchia commented Jul 25, 2025

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nilchia commented Jul 25, 2025

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nilchia commented Aug 2, 2025

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dianichj commented Aug 6, 2025

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