New tool : multiclassprediction by renu-pal · Pull Request #8041 · galaxyproject/tools-iuc

renu-pal · 2026-05-28T18:26:50Z

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.

bernt-matthias · 2026-05-28T18:39:54Z

All requirements should have a version.

bernt-matthias · 2026-05-28T18:40:19Z

This would be cool to have. Are you working on a conda recipe?

Hi @bernt-matthias , yes I am working on a recipe as well, but its getting some errors and I don't know why its not working . Can you have a look there if you get some time.
bioconda/bioconda-recipes#65121
Thanks !

bernt-matthias · 2026-05-28T18:41:29Z

paths need to be single quoted

bernt-matthias · 2026-05-28T18:42:25Z

I would prefer if the actual source code would be published separately. Is there a citation?

bernt-matthias · 2026-05-28T18:42:44Z

Use single quotes

bernt-matthias · 2026-05-28T18:43:52Z

The method, parameters and outputs need detailed description. Without citation this is rather a blackbox.

…akge

paulzierep

Change to multi omics capability.
More help needed.

paulzierep · 2026-07-07T09:51:46Z

+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@TOOL_VERSION@">multi-omics-classification</requirement>
+            <requirement type="package" version="1.5.2">scikit-learn</requirement>


I think we can remove all this requirements, they are all in the multi-omics-classification recipe

paulzierep · 2026-07-07T09:53:09Z

@@ -0,0 +1,7 @@
+scikit-learn


this file can be removed, this is handled by conda

paulzierep · 2026-07-07T09:53:33Z

@@ -0,0 +1,10 @@
+categories:
+- Machine Learning
+description: A FAIR Machine Learning Framework for Benchmarking, Feature Selection, and Hyperparameter Optimization of Machine Learning Models for Multiomics Data in Galaxy


Suggested change

description: A FAIR Machine Learning Framework for Benchmarking, Feature Selection, and Hyperparameter Optimization of Machine Learning Models for Multiomics Data in Galaxy

description: A Machine Learning Framework for Benchmarking, Feature Selection, and Hyperparameter Optimization of Machine Learning Models for Multiomics Data

paulzierep · 2026-07-07T09:54:24Z

+description: A FAIR Machine Learning Framework for Benchmarking, Feature Selection, and Hyperparameter Optimization of Machine Learning Models for Multiomics Data in Galaxy
+homepage_url: https://github.com/usegalaxy-eu/MultiOmicsClassification
+long_description: |
+ The MultiClassPrediction tool  is designed for multi-omics data analysis within the Galaxy platform,   enabling reproducible and standardized model evaluation across diverse biological datasets.


explain what it does, the galaxy part can be removed, we know its in galaxy :)

paulzierep · 2026-07-07T09:56:13Z

+
+    <inputs>
+
+        <param name="X" type="data" format="tabular" label="X: Input features" help="Feature matrix (independent variables used for prediction)"/>


explain input format, first row is feature names ?

paulzierep · 2026-07-07T09:57:54Z

+    </inputs>
+
+    <outputs>
+        <data name="output" format="csv" label="Multiclass AUC results"/>


can we ouput tabular ?

paulzierep · 2026-07-07T09:58:35Z

+            <param name="sampling_strategy" value="No Sampling"/>
+            <param name="grid_search" value="false"/>
+
+            <output name="output">


please add real test output, also for the plots and compare the files

paulzierep · 2026-07-07T09:59:04Z

+MultiClassPredict
+==================
+
+A FAIR Machine Learning Framework for Benchmarking, Feature Selection, and Hyperparameter Optimization of Machine Learning Models for Multiomics Data in Galaxy


we do not need FAIR and Galaxy ref, we know its in Galaxy which is FAIR :)

paulzierep · 2026-07-07T10:00:29Z

@@ -0,0 +1,178 @@
+<tool id="multi-omics-classification" name="multi-omics-classification" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>Multi Class prediction </description>


Suggested change

<description>Multi Class prediction </description>

<description>Multiomics Classification</description>

paulzierep · 2026-07-07T10:10:40Z

+
+    <inputs>
+
+        <param name="X" type="data" format="tabular" label="X: Input features" help="Feature matrix (independent variables used for prediction)"/>


Actually, we could make this a real multi-omics tool by making this a repeat, similar to

<repeat name="omics" min="0" title="Multiple omics layers?"> <param name="train_omics" type="data" optional="true" format="tabular" label="Training omics data"/> <param name="test_omics" type="data" optional="true" format="tabular" label="Test omics data"/> <param name="assay" type="text" optional="true" label="What type of assay is your input?" help="This would be used as output name."> <sanitizer invalid_char=" "> <valid initial="string.letters"> <add value="_"/> </valid> </sanitizer> </param> </repeat>

Then we can run the tool for each omics type using this as the label.
In the command line, one would need to merge X from all omics types once to create the combined input.

paulzierep

can you give the test-data better names, like prediction_results.csv (tabular would be better), also for the plots

multiclassprediction tools

1016e5a

github-project-automation Bot added this to Galaxy Tool Developers SIG Board May 28, 2026

github-project-automation Bot moved this to Triage/Discuss in Galaxy Tool Developers SIG Board May 28, 2026

bernt-matthias reviewed May 28, 2026

View reviewed changes

renu-pal and others added 16 commits May 29, 2026 18:20

paths in single quotes

a3acd97

adding shed.yml

8dae1df

Update .shed.yml

de8b2d5

adding versions

0f99642

Update .shed.yml

bbb46f2

reducing test input file size

d58620c

minor changes in python

f7533e2

lint issue in .py file

15e9278

renaming tool to multi-omics-classification

717a5c5

removing checkpoints

b094e3a

adding citation and help section

f3fb28d

updating url in shed file and linting issue in xml file

b3e8b9e

deleting python file from this folder and referencing to bioconda pac…

d0f285b

…akge

Merge branch 'galaxyproject:main' into mcp

3a5ff38

version update

f0b9540

adding output files in test folder manually

fd2a983

paulzierep reviewed Jul 7, 2026

View reviewed changes

	description: A FAIR Machine Learning Framework for Benchmarking, Feature Selection, and Hyperparameter Optimization of Machine Learning Models for Multiomics Data in Galaxy
	description: A Machine Learning Framework for Benchmarking, Feature Selection, and Hyperparameter Optimization of Machine Learning Models for Multiomics Data


		<inputs>

		<param name="X" type="data" format="tabular" label="X: Input features" help="Feature matrix (independent variables used for prediction)"/>

		@@ -0,0 +1,178 @@
		<tool id="multi-omics-classification" name="multi-omics-classification" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
		<description>Multi Class prediction </description>

	<description>Multi Class prediction </description>
	<description>Multiomics Classification</description>

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renu-pal commented May 28, 2026

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renu-pal May 31, 2026 •

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