--- a/metaquantome_filter.xml	Tue Dec 04 17:17:41 2018 -0500
+++ b/metaquantome_filter.xml	Wed Dec 05 14:37:17 2018 -0500
@@ -11,18 +11,20 @@
         --expand_file '$expand_file'
         --min_peptides $min_peptides 
         #if $min_pep_nsamp:
-            --min_pep_nsamp max($min_peptides,$min_pep_nsamp)
+            #set $nsamp = max(int($min_peptides),int($min_pep_nsamp))
+            --min_pep_nsamp $nsamp
         #else
             --min_pep_nsamp all
         #end if
         --min_children_non_leaf $min_children_non_leaf
         #if $min_child_nsamp:
-            --min_child_nsamp max($min_peptides,$min_child_nsamp)
+            #set $nsamp = max($min_peptides,$min_child_nsamp)
+            --min_child_nsamp $nsamp
         #else
             --min_child_nsamp all
         #end if
         --qthreshold $qthreshold
-        --outfile='$output'
+        --outfile='$outfile'
     ]]></command>
     <inputs>
         <expand macro="common_params"/>