diff --git a/tools/maaslin2/maaslin2.xml b/tools/maaslin2/maaslin2.xml
index c56fe2308dd..9b02af0511e 100644
--- a/tools/maaslin2/maaslin2.xml
+++ b/tools/maaslin2/maaslin2.xml
@@ -12,6 +12,7 @@
 ## can only return indices with type="data_column" 
 ## using awk so that the file is only parsed on command line execution
 
+#if $fixed_effects
 #set idx = []
 #for $i in $fixed_effects:
     #silent idx.append(f'${i}')
@@ -20,7 +21,10 @@
 
 fixed_effects=`awk -v OFS=',' -F"\t" 'NR == 1 { print $idx_for_awk}' '$input_metadata'` &&
 echo 'Assigned fixed effects as:' \$fixed_effects &&
+#end if
+
 
+#if $random_effects
 #set idx = []
 #for $i in $random_effects:
     #silent idx.append(f'${i}')
@@ -29,6 +33,7 @@ echo 'Assigned fixed effects as:' \$fixed_effects &&
 
 random_effects=`awk -v OFS=',' -F"\t" 'NR == 1 { print $idx_for_awk}' '$input_metadata'` &&
 echo 'Assigned random effects as:' \$random_effects &&
+#end if
 
 ln -s '$input_data' 'input_data.tsv'
 &&
@@ -79,9 +84,9 @@ cd outputFolder && mkdir -p figures/ && cp *.pdf figures
     <inputs>
         <param name="input_data" type="data" format="tabular" label="Data (or features) file"/>
         <param name="input_metadata" type="data" format="tabular" label="Metadata file"/>
-        <param argument="--fixed_effects" type="data_column" data_ref="input_metadata" use_header_names="true"  multiple="true" optional="true" label="Interactions: Fixed effects" help="The fixed effects for the model, comma-delimited for multiple effects" />
+        <param argument="--fixed_effects" type="data_column" data_ref="input_metadata" use_header_names="true"  multiple="true" optional="true" label="Interactions: Fixed effects" help="The fixed effects for the model, comma-delimited for multiple effects, Default value: All " />
         		
-        <param argument="--random_effects" type="data_column" data_ref="input_metadata" use_header_names="true" multiple="true" optional="true" label="Random effects" help="The random effects for the model,  comma-delimited for multiple effects" />
+        <param argument="--random_effects" type="data_column" data_ref="input_metadata" use_header_names="true" multiple="true" optional="true" label="Random effects" help="The random effects for the model,  comma-delimited for multiple effects, Default: None" />
         	
        
         	
@@ -108,7 +113,7 @@ cd outputFolder && mkdir -p figures/ && cp *.pdf figures
                 <option value="NEGBIN">NEGBIN</option>
                 <option value="ZINB">ZINB</option>
             </param>
-            <param argument="--correction" type="select" value="BH" multiple="true" optional="true" label="Correction" help="The correction method for computing  the q-value ">
+            <param argument="--correction" type="select" value="BH" optional="true" label="Correction" help="The correction method for computing  the q-value ">
                 <option value="holm">Holm</option>
                 <option value="hochberg">Hochberg</option>
                 <option value="hommel">Hommel</option>
@@ -332,6 +337,100 @@ cd outputFolder && mkdir -p figures/ && cp *.pdf figures
                 </element>                                                                    
             </output_collection>
         </test>   
+        <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" />
+            <section name="additional_options">
+                <param name="min_abundance" value="0.0"/>
+                <param name="min_prevalence" value="0.1"/>
+                <param name="max_significance" value="0.25"/>
+                <param name="normalization" value="TSS"/>
+                <param name="transform" value="LOG"/>
+                <param name="analysis_method" value="LM"/>
+                <param name="correction" value="BY"/>
+                <param name="standardize" value="True"/>
+            </section>
+            <section name="output">
+                <param name="plot_heatmap" value="true"/>
+                <param name="heatmap_first_n" value="50"/>
+                <param name="plot_scatter" value="true"/>
+                <param name="residuals_output" value="true"/>
+            </section>
+            <output name="all_results">
+                <assert_contents>
+                    <has_text text="feature"/>
+                    <has_n_lines n="8092"/>
+                    <has_n_columns n="9"/>
+                </assert_contents>
+            </output>
+            <output name="significant_results">
+                <assert_contents>
+                    <has_text text="subject"/>
+                    <has_n_lines n="213"/>
+                    <has_n_columns n="9"/>
+                </assert_contents>
+            </output>
+            <output name="residuals">
+                <assert_contents>
+                    <has_size value="671142" delta="1000"/>
+                </assert_contents>
+            </output>
+            <output_collection name="figures_pdfs" type="list">
+                <element name="heatmap.pdf" ftype="pdf">
+                    <assert_contents>
+                        <has_size value="7000" delta="1000" />
+                    </assert_contents>
+                </element>                                                              
+            </output_collection>
+        </test> 
+        <test expect_num_outputs="5">
+            <param name="input_data" value="HMP2_taxonomy.tsv"/>
+            <param name="input_metadata" value="HMP2_metadata.tsv"/>
+           
+            <section name="additional_options">
+                <param name="min_abundance" value="0.0"/>
+                <param name="min_prevalence" value="0.1"/>
+                <param name="max_significance" value="0.25"/>
+                <param name="normalization" value="TSS"/>
+                <param name="transform" value="LOG"/>
+                <param name="analysis_method" value="LM"/>
+                <param name="correction" value="BH"/>
+                <param name="standardize" value="True"/>
+            </section>
+            <section name="output">
+                <param name="plot_heatmap" value="true"/>
+                <param name="heatmap_first_n" value="50"/>
+                <param name="plot_scatter" value="true"/>
+                <param name="residuals_output" value="true"/>
+            </section>
+            <output name="all_results">
+                <assert_contents>
+                    <has_text text="feature"/>
+                    <has_n_lines n="8092"/>
+                    <has_n_columns n="9"/>
+                </assert_contents>
+            </output>
+            <output name="significant_results">
+                <assert_contents>
+                    <has_text text="subject"/>
+                    <has_n_lines n="880"/>
+                    <has_n_columns n="9"/>
+                </assert_contents>
+            </output>
+            <output name="residuals">
+                <assert_contents>
+                    <has_size value="670759" delta="1000"/>
+                </assert_contents>
+            </output>
+            <output_collection name="figures_pdfs" type="list">
+                <element name="heatmap.pdf" ftype="pdf">
+                    <assert_contents>
+                        <has_size value="7900" delta="1000" />
+                    </assert_contents>
+                </element>                                                              
+            </output_collection>
+        </test> 
     </tests>
     <help><![CDATA[
 @HELP_HEADER@
diff --git a/tools/maaslin2/macros.xml b/tools/maaslin2/macros.xml
index 335c4eca97a..b9646d382df 100644
--- a/tools/maaslin2/macros.xml
+++ b/tools/maaslin2/macros.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <macros>
-    <token name="@TOOL_VERSION@">1.7.3</token>
+    <token name="@TOOL_VERSION@">0.99.12</token>
     <token name="@VERSION_SUFFIX@">0</token>
     <token name="@PROFILE@">20.01</token>
     <xml name="edam_ontology">