Add MAGs-visualization Galaxy wrappers by alexandrah1704 · Pull Request #7922 · galaxyproject/tools-iuc

alexandrah1704 · 2026-04-26T14:10:42Z

This PR adds Galaxy wrappers for MAGs-visualization, a toolkit for generating plots and dashboards for MAG evaluation results (CheckM, CheckM2, dRep, GTDB, QUAST, Bakta, CoverM, metadata, KEGG).

This PR supersedes my previous submission (#7583).

The previous single-wrapper implementation has been refactored into separate, modular wrappers for each subcommand.

The following tools are included:

comp-conta
sample-heatmap
drep-cluster-annot
drep-cluster-func
pathway-module-heatmap

It supports multiple visualization types (quality metrics, taxonomy, clustering, abundance, functional annotation).
Outputs returned as dataset collections.
Links to example outputs included in help sections.

The wrappers use the mags-visualizationCLI distributed via Bioconda:
https://github.com/bioconda/bioconda-recipes/tree/master/recipes/mags-visualization

Source code:
https://github.com/usegalaxy-eu/MAGs-visualization

Tested locally with planemo test.
All local builds and tests pass.

Example outputs can be found in the MAGs-visualization use cases:
https://github.com/usegalaxy-eu/MAGs-visualization/tree/main/use-cases

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)

alexandrah1704 · 2026-04-26T17:52:44Z

Adjusted pathway test dataset size to ensure meaningful heatmap visualization while staying within IUC file size limits.

SaimMomin12

Thanks @alexandrah1704

Some preliminary comments inline

SaimMomin12 · 2026-04-27T08:39:08Z

@@ -0,0 +1,167 @@
+<tool id="mags_visualization_comp_conta" name="MAGs-visualization comp-conta" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05">


Suggested change

<tool id="mags_visualization_comp_conta" name="MAGs-visualization comp-conta" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05">

<tool id="mags_visualization_comp_conta" name="MAGs-visualization comp-conta" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">

SaimMomin12 · 2026-04-27T08:39:52Z

+        <param name="checkm" type="data" format="tabular,tsv" label="CheckM results" />
+        <param name="checkm2" type="data" format="tabular,tsv" label="CheckM2 results" />


Can we prefer either tabular or tsv here?

SaimMomin12 · 2026-04-27T08:40:49Z

+    </outputs>
+
+    <tests>
+        <test>


Suggested change

<test>

<test expect_num_outputs="1">

Please add this all tests

SaimMomin12 · 2026-04-27T08:41:45Z

+        <param name="checkm" type="data" format="tabular,tsv" label="CheckM results" />
+        <param name="checkm2" type="data" format="tabular,tsv" label="CheckM2 results" />
+
+        <conditional name="mode">


Would prefer different conditional name as its similar to the below param name

SaimMomin12 · 2026-04-27T08:42:22Z

+    <help><![CDATA[
+**MAGs-visualization: comp-conta**
+


A more detailed help would be nice to have

SaimMomin12 · 2026-04-27T08:47:01Z

+        </param>
+
+        <param name="max_col" type="integer" value="10" min="1" label="Maximum number of taxonomy labels" />
+        <param name="no_log" type="boolean" checked="false" truevalue="true" falsevalue="" label="Disable log10 scaling for the top bar plot" />


Suggested change

<param name="no_log" type="boolean" checked="false" truevalue="true" falsevalue="" label="Disable log10 scaling for the top bar plot" />

<param name="no_log" type="boolean" checked="false" truevalue="--no_log" falsevalue="" label="Disable log10 scaling for the top bar plot" />

SaimMomin12 · 2026-04-27T08:47:19Z

+        #if $no_log
+            --no_log
+        #end if


Suggested change

#if $no_log

--no_log

#end if

$no_log

SaimMomin12 · 2026-04-27T08:47:39Z

@@ -0,0 +1,80 @@
+<tool id="mags_visualization_taxa_sankey" name="MAGs-visualization taxa-sankey" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05">


Suggested change

<tool id="mags_visualization_taxa_sankey" name="MAGs-visualization taxa-sankey" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05">

<tool id="mags_visualization_taxa_sankey" name="MAGs-visualization taxa-sankey" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">

alexandrah1704 · 2026-04-27T15:45:18Z

Thank you for the detailed review.

I have applied all comments:

updated XML formatting using planemo format
used profile tokens
improved help sections with clearer descriptions
$no_log
renamed conditional mode into mode_cond
added expect_num_outputs
just used tabular

Please let me know if anything else should be adjusted.

bernt-matthias

Great start. Some more comments from my side. Some apply to multiple/all tools.

bernt-matthias · 2026-04-30T07:14:10Z

+                <param name="meta_bin_width" type="float" value="5.0" label="Bin width for numeric metadata"/>
+            </when>
+        </conditional>
+        <param name="top_n" type="integer" value="30" min="1" label="Top N categories"/>


Categories of what?

bernt-matthias · 2026-04-30T07:15:30Z

+        </section>
+    </inputs>
+    <outputs>
+        <collection name="plots" type="list" label="${tool.name} outputs">


If there is only one output you should stick to the default label. Otherwise use the prefix ${tool.name} on ${on_string}. The suffix outputs is definitely not needed - clearly its outputs :)

bernt-matthias · 2026-04-30T07:16:19Z

+            <param name="checkm2" value="checkm2.tsv"/>
+            <param name="format" value="png"/>
+            <output_collection name="plots" type="list">
+                <element name="comp_conta_marginals_checkm">


Please add ftype to the outputs.

For images (png) we have assertions on width and height that could be used here.

bernt-matthias · 2026-04-30T07:16:51Z

+            <param name="mode_cond|mode" value="tax"/>
+            <param name="mode_cond|gtdb" value="gtdb.tsv"/>
+            <param name="tax_level" value="phylum"/>
+            <param name="format" value="png"/>


Can you adapt tests 2 and 3 to test for pdf and svg output?

bernt-matthias · 2026-04-30T07:19:09Z

+            </when>
+            <when value="meta">
+                <param name="metadata" type="data" format="tabular" label="Metadata table"/>
+                <param name="meta_col" type="text" label="Metadata column name"/>


Maybe a data_column https://docs.galaxyproject.org/en/master/dev/schema.html#data-column parameter would be an option?

bernt-matthias · 2026-04-30T07:19:30Z

+            <when value="meta">
+                <param name="metadata" type="data" format="tabular" label="Metadata table"/>
+                <param name="meta_col" type="text" label="Metadata column name"/>
+                <param name="meta_bin_width" type="float" value="5.0" label="Bin width for numeric metadata"/>


Add min and/or max to numeric parameters if possible.

bernt-matthias · 2026-04-30T07:20:46Z

+        <repeat name="tax_levels" title="Taxonomy levels" min="2">
+            <param name="level" type="select" label="Taxonomic level">
+                <option value="domain">domain</option>
+                <option value="phylum" selected="true">phylum</option>
+                <option value="class">class</option>
+                <option value="order">order</option>
+                <option value="family">family</option>
+                <option value="genus" selected="true">genus</option>
+                <option value="species">species</option>
+            </param>
+        </repeat>


Replace by a select with multiple="true"?

bernt-matthias · 2026-04-30T07:22:00Z

+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="drep" value="drep.csv"/>


Can you also test with a tabular input?

bernt-matthias · 2026-04-30T07:23:13Z

+            <repeat name="meta_cols" title="Metadata columns" min="0">
+                <param name="col" type="text" label="Metadata column name"/>
+            </repeat>


data_column with multiple="true"?

bgruening · 2026-05-01T16:10:09Z

There is a new version available

alexandrah1704 · 2026-05-04T13:05:26Z

Thank you for the review.
I have now implemented the requested changes.
Please let me know if any further adjustements are needed.

bgruening · 2026-05-06T12:16:52Z

Hi @alexandrah1704!

Thanks a lot, a few comments:

The command block has a copy-paste error: the #if $mode_cond.mode == "tax" conditional appears twice. The second block re-emits --gtdb without --tax_level, which will pass the flag twice and may cause CLI errors.

#if $mode_cond.mode == "tax"
    --gtdb '$mode_cond.gtdb'
    --tax_level '$mode_cond.tax_level'
#end if

#if $mode_cond.mode == "tax"   <!-- DUPLICATE — remove this block? -->
    --gtdb '$mode_cond.gtdb'
#end if

The --tax_levels loop is emitted after the -o outputs argument, which produces a malformed command. If tax_levels is an empty list this also creates a dangling --tax_levels with no values.
Using len() on a Cheetah repeat variable to guard meta_cols is unreliable in Galaxy templates. The current pattern:

#if $metadata_cond.metadata and len($metadata_cond.meta_cols) > 0

Fix: Use the standard idiom:

#if $metadata_cond.metadata
    --metadata '$metadata_cond.metadata'
    #if $metadata_cond.meta_cols
        --meta_cols
        #for $mc in $metadata_cond.meta_cols
            '$mc.col'
        #end for
    #end if
#end if

The output collection pattern matches html|png|pdf|svg but there is no --format flag is this working or is the tool using a standard format?
consider adding a argument= attribute on <param> elements
If a DOI or Zenodo record exists, prefer type="doi" over a raw BibTeX entry
Most tests only assert a minimum, please use stronger assertions and better tests.

<assert_contents>
    <has_size min="1"/>
</assert_contents>

e.g.

<has_image_width min="100"/>
<has_image_height min="100"/>

For SVG outputs, has_text on expected axis labels would be appropriate. For PDFs, assert a realistic minimum file size.

The first test case specifies tax_levels as two separate <param> elements:

<param name="tax_levels" value="phylum"/>
<param name="tax_levels" value="genus"/>

You can have multiple selections, correct? This:

<param name="tax_levels" value="phylum,genus"/>

Only one test case exists (rank=phylum). At least one additional rank (e.g., genus) should be tested.
Free-text meta_col / meta_cols parameters in comp_conta.xml and sample_heatmap.xml are passed directly to the CLI:

<param name="meta_col" type="text" label="Metadata column name"/>

Galaxy's single-quoting prevents shell injection, but column names containing commas or semicolons could affect parsing inside the Python tool. Please add a <sanitizer> block, or switch to data_column type to restrict input to valid column names from the dataset.

paulzierep

need to continue later

paulzierep · 2026-05-13T11:47:25Z

+        </section>
+    </inputs>
+    <outputs>
+        <collection name="plots" type="list">


you do not need collection output here, since each tool produces only one output afaik, since file name are variable you could do

cp outputs/${dynamic_name}.png outputs/final_plot.png

on the command line and then

<data name="plot" format="png" from_work_dir="outputs/final_plot.png"/>

Please adapt for all tools.

paulzierep · 2026-05-13T11:49:46Z

+            <option value="variance">variance (differential modules)</option>
+            <option value="both">both</option>
+        </param>
+        <param argument="--format" type="select" label="Output format">


you have format and fig size for all tools, you could move that to the macros and then add unit to the help, also add min, max please

paulzierep · 2026-05-13T11:53:23Z

+                    label="Metadata column"
+                    use_header_names="true"
+                    help="Select the column to color by"/>
+                <param name="meta_bin_width" type="float" value="5.0" min="0.1" label="Bin width for numeric metadata"/>


needs more explanation

paulzierep · 2026-05-13T11:54:39Z

+
+This tool visualizes genome clusters generated by dRep and annotates them using GTDB taxonomy.
+
+Clusters are grouped by taxonomic levels (e.g. phylum, genus) based on representative genomes.


are they grouped ?

paulzierep · 2026-05-13T11:57:00Z

+        </param>
+        <section name="representatives" title="Representative MAG selection (optional)" expanded="false">
+            <param name="drep" type="data" format="csv,tabular" optional="true" label="dRep cluster table"/>
+            <param name="gtdb" type="data" format="tabular" optional="true" label="GTDB annotation table"/>


why is gtdb needed for selection ?

gtdb is needed to select the same representative genomes as in the drep-cluster-func plot. Without gtdb, there will be a different row order and different MAGs being shown. With gtdb both plots show identical MAGs in the same order, to make it directly comparable, so there is no confusion.

You could add a bit of help, eg via the help attribute what these inputs are used for / in which cases the user should supply them.

alexandrah1704 · 2026-05-20T09:20:52Z

I've adjusted the following:

Removed duplicate
used standard idom for metadata_cond.metadata
there is now a format flag in taxa_sankey, which will work for all outputs (png, pdf svg) with the new version v0.0.9, once its merged in bioconda.
added argument in
adjusted tests
data_column is now used for metadata
removed collection
moved fig_size and format to macros
checkm, checkm2 can now be plotted separately

Add MAGs-visualization Galaxy wrappers

28ef722

alexandrah1704 mentioned this pull request Apr 26, 2026

Add mags visualization tool #7583

Closed

5 tasks

Adjust pathway test data for better visualization and minimized

88934d8

SaimMomin12 reviewed Apr 27, 2026

View reviewed changes

Address review comments: improve help, update tests, xml formatting

06e4279

bernt-matthias reviewed Apr 30, 2026

View reviewed changes

Adjusted xml files

c8b119a

test

dd3e4c4

paulzierep reviewed May 13, 2026

View reviewed changes

Adjustment_2.0

a328527

		@@ -0,0 +1,167 @@
		<tool id="mags_visualization_comp_conta" name="MAGs-visualization comp-conta" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05">

		<param name="checkm" type="data" format="tabular,tsv" label="CheckM results" />
		<param name="checkm2" type="data" format="tabular,tsv" label="CheckM2 results" />

	<param name="no_log" type="boolean" checked="false" truevalue="true" falsevalue="" label="Disable log10 scaling for the top bar plot" />
	<param name="no_log" type="boolean" checked="false" truevalue="--no_log" falsevalue="" label="Disable log10 scaling for the top bar plot" />

		@@ -0,0 +1,80 @@
		<tool id="mags_visualization_taxa_sankey" name="MAGs-visualization taxa-sankey" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05">


		This tool visualizes genome clusters generated by dRep and annotates them using GTDB taxonomy.

		Clusters are grouped by taxonomic levels (e.g. phylum, genus) based on representative genomes.

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alexandrah1704 commented Apr 26, 2026

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alexandrah1704 commented Apr 27, 2026

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bgruening commented May 1, 2026

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alexandrah1704 May 20, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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alexandrah1704 commented May 20, 2026

alexandrah1704 May 20, 2026 •

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