--- a/mmuphin.xml	Tue Feb 25 21:25:45 2025 +0000
+++ b/mmuphin.xml	Fri May 16 12:56:52 2025 +0000
@@ -65,7 +65,8 @@
         
         # Save results into output files
 
-        write.table(result\$feature_abd_adj, file="$output", quote = FALSE, sep="\t")
+        write.table(result\$feature_abd_adj, file="$output", quote = FALSE, sep="\t", col.names=NA)
+
     ]]></configfile>
         </configfiles>
  
@@ -79,7 +80,7 @@
             <param argument="pseudo_count" type="float" optional="true" label="Pseudo_count" help="Pseudo count to add feature_abd before the methods' log transformation. Default to the half of the minimal non-zero values in feature_abd" />
             <param argument="conv" type="float" value="0.0001"  min="0.000001" max="0.001" optional="true" label="Convergence threshold" help="Convergence threshold for the method's iterative algorithm for shrinking batch effect parameters."/>
             <param argument="maxit" type="float" optional="true" value="1000" label="Maximum number of iterations" help="Maximum number of iterations allowed for the method's iterative algorithm. Default to 1000"/>
-            <param argument="verbose" type="hidden" truevalue="verbose TRUE" falsevalue="verbose FALSE" checked="true" label="Print verbose information"/> 
+            <param argument="verbose" type="hidden" value="False" label="Print verbose information"/> 
             <param argument="diagnostic_plot" type="boolean" truevalue="diagnostic_plot TRUE" falsevalue="diagnostic_plot FALSE" checked="true"  label="Generate diagnostic figure file"/>
          </section>
     </inputs>
@@ -100,11 +101,11 @@
             <param name="batch_input" value="29"/> 
             <param name="covariates_input" value="4"/> 
             <section name="additional_options">
-                <param name="zero_inflation" value="TRUE"/>
+                <param name="zero_inflation" value="True"/>
                 <param name="pseudo_count" value="3"/>
                 <param name="conv" value="0.0001"/>
                 <param name="maxit" value="1000"/>
-                <param name="diagnostic_plot" value="TRUE"/>
+                <param name="diagnostic_plot" value="True"/>
             </section>
             <output name="output" file="CRC_abd_corrected.tsv" ftype="tabular"/>
             <output name="diagnostic_plot_output" file="diagnostic.pdf" ftype="pdf"/>          
@@ -114,11 +115,11 @@
             <param name="input_metadata" value="CRC_meta.tsv"/>
             <param name="batch_input" value="7"/> 
             <section name="additional_options">
-                <param name="zero_inflation" value="TRUE"/>
+                <param name="zero_inflation" value="True"/>
                 <param name="pseudo_count" value="3"/>
                 <param name="conv" value="0.0001"/>
                 <param name="maxit" value="1000"/>
-                <param name="diagnostic_plot" value="TRUE"/>
+                <param name="diagnostic_plot" value="True"/>
             </section>
             <output name="output" file="CRC_abd_corrected2.tsv" ftype="tabular"/>
             <output name="diagnostic_plot_output" file="diagnostic2.pdf" ftype="pdf"/>          
@@ -129,11 +130,11 @@
             <param name="batch_input" value="29"/>
             <param name="covariates_input" value="4,6"/> 
             <section name="additional_options">
-                <param name="zero_inflation" value="TRUE"/>
+                <param name="zero_inflation" value="True"/>
                 <param name="pseudo_count" value="3"/>
                 <param name="conv" value="0.0001"/>
                 <param name="maxit" value="1000"/>
-                <param name="diagnostic_plot" value="TRUE"/>
+                <param name="diagnostic_plot" value="True"/>
             </section>
             <output name="output" file="CRC_abd_corrected3.tsv" ftype="tabular"/>
             <output name="diagnostic_plot_output" file="diagnostic3.pdf" ftype="pdf"/>