galaxyproject · SantaMcCloud · Sep 8, 2025 · Sep 8, 2025 · Sep 8, 2025 · Sep 8, 2025
diff --git a/tools/maaslin3/.shed.yml b/tools/maaslin3/.shed.yml
@@ -0,0 +1,15 @@
+name: maaslin3
+owner: iuc
+description: "MaAsLin 3 is the next generation of MaAsLin. This comprehensive R package efficiently determines multivariable associations between clinical metadata and microbial meta-omics features."
+homepage_url: https://github.com/biobakery/maaslin3
+long_description: |
+    MaAsLin 3 is the next generation of MaAsLin (Microbiome Multivariable Associations with Linear Models). 
+    This comprehensive R package efficiently determines multivariable associations between clinical metadata 
+    and microbial meta-omics features. Relative to MaAsLin 2, MaAsLin 3 introduces the ability to quantify 
+    and test for both abundance and prevalence associations while accounting for compositionality.
+    By incorporating generalized linear models, MaAsLin 3 accomodates most modern epidemiological study 
+    designs including cross-sectional and longitudinal studies.
+remote_repository_url: https://github.com/biobakery/maaslin3
+type: unrestricted
+categories:
+  - Metagenomics
diff --git a/tools/maaslin3/maaslin3.xml b/tools/maaslin3/maaslin3.xml
diff --git a/tools/maaslin3/macros.xml b/tools/maaslin3/macros.xml
@@ -0,0 +1,11 @@
+<?xml version="1.0"?>
+<macros>
+    <token name="@TOOL_VERSION@">0.99.16</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@PROFILE@">25.0</token>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@TOOL_VERSION@">maaslin3</requirement>
+        </requirements>
+    </xml>
+ </macros>
diff --git a/tools/maaslin3/test-data/HMP2_metadata.tsv b/tools/maaslin3/test-data/HMP2_metadata.tsv
diff --git a/tools/maaslin3/test-data/HMP2_taxonomy.tsv b/tools/maaslin3/test-data/HMP2_taxonomy.tsv
diff --git a/tools/maaslin3/test-data/age_Alistipes_SGB2313_logistic.png b/tools/maaslin3/test-data/age_Alistipes_SGB2313_logistic.png
diff --git a/tools/maaslin3/test-data/all_results.tsv b/tools/maaslin3/test-data/all_results.tsv
diff --git a/tools/maaslin3/test-data/data_transformed.tsv b/tools/maaslin3/test-data/data_transformed.tsv
diff --git a/tools/maaslin3/test-data/fitted_linear.rds b/tools/maaslin3/test-data/fitted_linear.rds
diff --git a/tools/maaslin3/test-data/significant_results.tsv b/tools/maaslin3/test-data/significant_results.tsv
diff --git a/tools/maaslin3/test-data/summary_plot.pdf b/tools/maaslin3/test-data/summary_plot.pdf
diff --git a/tools/maaslin3/test-data/summary_plot.png b/tools/maaslin3/test-data/summary_plot.png
diff --git a/tools/maaslin3/test-data/summary_plot_gg.RDS b/tools/maaslin3/test-data/summary_plot_gg.RDS