--- a/summarize_taxa.xml	Sat Aug 05 07:59:24 2017 -0400
+++ b/summarize_taxa.xml	Mon Oct 16 05:02:19 2017 -0400
@@ -17,10 +17,10 @@
     $md_as_string
     $absolute_abundance
     #if str( $lower_percentage )
-        -l '$lower_percentage'
+        -l $lower_percentage
     #end if
     #if str( $upper_percentage)
-        -u '$upper_percentage'
+        -u $upper_percentage
     #end if
     $transposed_output
     $suppress_classic_table_output
@@ -42,7 +42,7 @@
         <param argument="--md_as_string" type="boolean" truevalue="--md_as_string" falsevalue="" checked="false" label="Include metadata as string?" help="By default, metadata is included as list"/>
         <param argument="--absolute_abundance" type="boolean" truevalue="--absolute_abundance" falsevalue="" checked="false" label="Report absolute abundance?" help="By default, relative abundance is reported"/>
         <param argument="--lower_percentage" type="float" value="" optional="true" label="Percentage threshold to remove highly present OTU" help="If present, OTUs having higher absolute abundance are trimmed. To remove OTUs that make up more than 5% of the total dataset you would pass 0.05"/>
-        <param argument="--upper_percentage" type="float" value="" label="Percentage threshold to remove lowly present OTU" help="If present, OTUs having lower absolute abundance are trimmed. To remove the OTUs that makes up less than 45% of the total dataset you would pass 0.45"/>
+        <param argument="--upper_percentage" type="float" value="" optional="true" label="Percentage threshold to remove lowly present OTU" help="If present, OTUs having lower absolute abundance are trimmed. To remove the OTUs that makes up less than 45% of the total dataset you would pass 0.45"/>
         <param argument="--transposed_output" type="boolean" truevalue="--transposed_output" falsevalue="" checked="false" label="Transpose output?" help="If checked, the output will be written transposed from the regular output. This is helpful in cases when you want to use Site Painter to visualize your data"/>
         <param argument="--suppress_classic_table_output" type="boolean" truevalue="--suppress_classic_table_output" falsevalue="" checked="false" label="Suppress creation of the classic (TSV) format taxon table?" help="This option is ignored if a mapping file is present"/>
         <param argument="--suppress_biom_table_output" type="boolean" truevalue="--suppress_biom_table_output" falsevalue="" checked="false" label="Suppress creation of the BIOM-formatted taxon table?" help="This option is ignored if a mapping file is present"/>