maaslin2 : updated fixed and random effects to include just numbers i…

…n tests
galaxyproject · Apr 24, 2024 · 02ab4b6 · 02ab4b6
1 parent bfc500c
commit 02ab4b6
Showing 1 changed file with 5 additions and 5 deletions.
diff --git a/tools/maaslin2/maaslin2.xml b/tools/maaslin2/maaslin2.xml
@@ -148,8 +148,8 @@ cd outputFolder && mkdir -p figures/ && cp *.pdf figures
         <test expect_num_outputs="5">
             <param name="input_data" value="HMP2_taxonomy.tsv"/>
             <param name="input_metadata" value="HMP2_metadata.tsv"/>
-            <param name="random_effects" value= "c2: site,c5: subject"/> 
-            <param name="fixed_effects" value="c4: diagnosis,c9: dysbiosisnonIBD,c10: dysbiosisUC,c11: dysbiosisCD,c6: antibiotics,c3: age"/> 
+            <param name="random_effects" value= "2,5"/> 
+            <param name="fixed_effects" value="4,9,10,11,6,3"/> 
             <section name="additional_options">
                 <param name="min_abundance" value="0.0"/>
                 <param name="min_prevalence" value="0.1"/>
@@ -231,7 +231,7 @@ cd outputFolder && mkdir -p figures/ && cp *.pdf figures
         <test expect_num_outputs="5">
             <param name="input_data" value="HMP2_taxonomy.tsv"/>
             <param name="input_metadata" value="HMP2_metadata.tsv"/>
-            <param name="fixed_effects" value="c4: diagnosis,c9: dysbiosisnonIBD"/>
+            <param name="fixed_effects" value="4,9"/>
             <section name="additional_options">
                 <param name="min_abundance" value="0.0"/>
                 <param name="min_prevalence" value="0.1"/>
@@ -278,7 +278,7 @@ cd outputFolder && mkdir -p figures/ && cp *.pdf figures
         <test expect_num_outputs="5">
             <param name="input_data" value="HMP2_taxonomy.tsv"/>
             <param name="input_metadata" value="HMP2_metadata.tsv"/>
-            <param name="fixed_effects" value="c4: diagnosis,c9: dysbiosisnonIBD"/>
+            <param name="fixed_effects" value="4,9"/>
             <section name="additional_options">
                 <param name="min_abundance" value="0.0001"/>
                 <param name="min_prevalence" value="0.1"/>
@@ -340,7 +340,7 @@ cd outputFolder && mkdir -p figures/ && cp *.pdf figures
         <test expect_num_outputs="5">
             <param name="input_data" value="HMP2_taxonomy.tsv"/>
             <param name="input_metadata" value="HMP2_metadata.tsv"/>
-            <param name="random_effects" value="c3: age" />
+            <param name="random_effects" value="3" />
             <section name="additional_options">
                 <param name="min_abundance" value="0.0"/>
                 <param name="min_prevalence" value="0.1"/>