From 02ab4b6ef3b41f1eda8fd6e7a6f1652f3fb2ba5f Mon Sep 17 00:00:00 2001
From: RENU <renu244pal@gmail.com>
Date: Wed, 24 Apr 2024 19:46:29 +0200
Subject: [PATCH] maaslin2 : updated fixed and random effects to include just
 numbers in tests

---
 tools/maaslin2/maaslin2.xml | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/tools/maaslin2/maaslin2.xml b/tools/maaslin2/maaslin2.xml
index 9b02af0511e..fa5a9f220d2 100644
--- 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"/>