Add MaAsLin3 #7263

SantaMcCloud · 2025-09-08T08:44:24Z

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)

SaimMomin12

Some preliminary comments inline

tools/maaslin3/.shed.yml

tools/maaslin3/maaslin3.xml

SantaMcCloud · 2025-09-26T15:52:51Z

@SaimMomin12 you can Review it again. The test and linting didnt errored so i don know why the complet WF got an error.

bgruening · 2025-09-28T06:40:11Z

Its green now, the failing summary was just a one-off.

SantaMcCloud · 2025-09-28T11:14:51Z

Its green now, the failing summary was just a one-off.

okay thank you i had it at an other PR aswell so i wasnt sure about it.

SantaMcCloud · 2025-10-15T16:00:06Z

@SaimMomin12 can you also review this please? :)

SaimMomin12

Some comments inline. Please try to use Galaxy Language Server extension for proper indentations of the XML.

SaimMomin12 · 2025-10-15T18:58:32Z

tools/maaslin3/maaslin3.xml

+        <param argument="--fixed_effects" type="data_column" data_ref="input_metadata" use_header_names="true" multiple="true" optional="true" label="Set fix effects"
+            help="Select the fix effects for the model. DEFAULT: ALL"/>


Suggested change

<param argument="--fixed_effects" type="data_column" data_ref="input_metadata" use_header_names="true" multiple="true" optional="true" label="Set fix effects"

help="Select the fix effects for the model. DEFAULT: ALL"/>

<param argument="--fixed_effects" type="data_column" data_ref="input_metadata" use_header_names="true" multiple="true" optional="true" label="Set fix effects" help="Select the fix effects for the model. DEFAULT: ALL"/>

tools/maaslin3/maaslin3.xml

SaimMomin12 · 2025-10-15T18:59:31Z

tools/maaslin3/maaslin3.xml

+        <param argument="--group_effects" type="data_column" data_ref="input_metadata" use_header_names="true" multiple="true" optional="true" label="Set group effects"
+            help="Select group effects for the model. DEFAULT: NONE"/>


Suggested change

<param argument="--group_effects" type="data_column" data_ref="input_metadata" use_header_names="true" multiple="true" optional="true" label="Set group effects"

help="Select group effects for the model. DEFAULT: NONE"/>

<param argument="--group_effects" type="data_column" data_ref="input_metadata" use_header_names="true" multiple="true" optional="true" label="Set group effects" help="Select group effects for the model. DEFAULT: NONE"/>

SaimMomin12 · 2025-10-15T18:59:57Z

tools/maaslin3/maaslin3.xml

+        <param argument="--ordered_effects" type="data_column" data_ref="input_metadata" use_header_names="true" multiple="true" optional="true" label="Set ordered effects"
+            help="Select the ordered effects for the model. DEFAULT: NONE"/>


Suggested change

<param argument="--ordered_effects" type="data_column" data_ref="input_metadata" use_header_names="true" multiple="true" optional="true" label="Set ordered effects"

help="Select the ordered effects for the model. DEFAULT: NONE"/>

<param argument="--ordered_effects" type="data_column" data_ref="input_metadata" use_header_names="true" multiple="true" optional="true" label="Set ordered effects" help="Select the ordered effects for the model. DEFAULT: NONE"/>

Can you please correct all the indentation issues?

SaimMomin12 · 2025-10-15T19:00:44Z

tools/maaslin3/maaslin3.xml

+        <param argument="--strata_effects" type="data_column" data_ref="input_metadata" use_header_names="true" optional="true" label="Set strata effects"
+            help="Select only one strata effect for the model. DEFAULT: NONE"/>
+        <section name="options" title="Additional options" expanded="true">
+            <param argument="--min_abundance" type="integer" value="0" label="Minimum abundance"
+                help="Minimum abundance for each feature befor normalization and transformation"/>
+            <param argument="--min_prevalence" type="integer" value="0" label="Mimimum prevalence"
+                help="The minimum proportion of samples for which a feature is detected at minimum abundance"/>
+            <param argument="--zero-threshold" type="integer" value="0" label="Zero threshold"
+                help="The minimum abundance to be considered non-zero"/>
+            <param argument="--min_variance" type="integer" value="0" label="Minimum variance"
+                help="Keep features with variances greater than value"/>
+            <param argument="--max_significance" type="float" value="0.1" label="Maximum significance"
+                help="The q-value threshold for significance"/>


identification

I dont know what you mean by this sorry

the help label here is on a new line instead of the same param line. I mean can you have entire param line along with help in same line for eg

<param argument="--max_significance" type="float" value="0.1" label="Maximum significance" help="The q-value threshold for significance"/>

Oh okay this should be fix with the first commit i did. i normally did it like this but if the style it chnage i will keep it into 1 line per Parameter!

tools/maaslin3/maaslin3.xml

SaimMomin12 · 2025-10-15T19:01:35Z

tools/maaslin3/maaslin3.xml

+            <param argument="--standardize" type="boolean" truevalue="--standardize TRUE" falsevalue="" checked="true" label="Standardize"
+                help="Apply z-score so continuous metadata are on the same scale"/>


indentation

8368477 i hope i did unterstand you correctlly

tools/maaslin3/maaslin3.xml

tools/maaslin3/macros.xml

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

…into maaslin3

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

SantaMcCloud · 2025-10-15T19:29:42Z

I hope i did fix evreything now beside of the one thing which i dont know what you mean by it

SantaMcCloud added 4 commits September 8, 2025 10:43

Add MaAsLin3

6882351

fix command line

f576ead

fix complete command line

6815beb

fix tool error

11b16e3

SaimMomin12 reviewed Sep 16, 2025

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SantaMcCloud and others added 7 commits September 17, 2025 11:53

change one input param and did reviewed changes

c82a22f

Update command line

a013af1

Update repeat test input

ff2c625

command line

3f56e42

Update maaslin3.xml

6c3b286

some changes

ed3116d

make it work

2e28d16

SantaMcCloud mentioned this pull request Sep 30, 2025

add COMEBin utility script #7285

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SaimMomin12 reviewed Oct 15, 2025

View reviewed changes

SantaMcCloud and others added 6 commits October 15, 2025 21:18

auto format

90579af

Update tools/maaslin3/maaslin3.xml

a6c52d3

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

indentation

8368477

Merge branch 'maaslin3' of https://github.com/SantaMcCloud/tools-iuc …

55c3977

…into maaslin3

Update tools/maaslin3/macros.xml

838245c

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

Update tools/maaslin3/maaslin3.xml

9e86d13

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

		<param argument="--fixed_effects" type="data_column" data_ref="input_metadata" use_header_names="true" multiple="true" optional="true" label="Set fix effects"
		help="Select the fix effects for the model. DEFAULT: ALL"/>

		<param argument="--group_effects" type="data_column" data_ref="input_metadata" use_header_names="true" multiple="true" optional="true" label="Set group effects"
		help="Select group effects for the model. DEFAULT: NONE"/>

		<param argument="--ordered_effects" type="data_column" data_ref="input_metadata" use_header_names="true" multiple="true" optional="true" label="Set ordered effects"
		help="Select the ordered effects for the model. DEFAULT: NONE"/>

		<param argument="--standardize" type="boolean" truevalue="--standardize TRUE" falsevalue="" checked="true" label="Standardize"
		help="Apply z-score so continuous metadata are on the same scale"/>

Add MaAsLin3 #7263

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SantaMcCloud commented Sep 8, 2025

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SantaMcCloud commented Sep 26, 2025

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SantaMcCloud commented Sep 28, 2025

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SantaMcCloud commented Oct 15, 2025

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SantaMcCloud commented Oct 15, 2025

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