--- a/repeatmasker.xml	Fri Aug 27 09:16:08 2021 +0000
+++ b/repeatmasker.xml	Thu Oct 21 15:49:31 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="repeatmasker_wrapper" name="RepeatMasker" version="@TOOL_VERSION@+@GALAXY_TOOL_VERSION@" profile="20.01">
+<tool id="repeatmasker_wrapper" name="RepeatMasker" version="@TOOL_VERSION@+@VERSION_SUFFIX@" profile="20.01">
     <description>screen DNA sequences for interspersed repeats and low complexity regions</description>
     <macros>
         <import>macros.xml</import>
@@ -58,7 +58,7 @@
     ${advanced.keep_alignments}
     ${advanced.invert_alignments}
     ${advanced.xout}
-    ${advanced.xsmall}
+    ${xsmall}
     ${advanced.poly}
     rm_input.fasta &&
     #if $advanced.is_only != '-is_only':
@@ -124,6 +124,7 @@
     </conditional>
     <param type="boolean" argument="-gff" truevalue="-gff" falsevalue="" label="Output annotation of repeats in GFF format" checked="false" />
     <param argument="-excln" type="boolean" truevalue="-excln" falsevalue="" label="Ignore stretches of Ns when computing statistics" checked="true" help="Scaffolds are sometimes joined with stretches of 25 or more Ns. This option ignores them when calculating repeat statistics" />
+    <param type="boolean" argument="-xsmall" truevalue="-xsmall" falsevalue="" checked="false" label="Perform softmasking instead of hardmasking" help="Output repetitive regions as lowercase, non-repetitive regions as uppercase (instead of replacing repetitive regions with 'N's)" />
     <section name="advanced" title="Advanced options" expanded="false">
       <param argument="-is_only" type="boolean" truevalue="-is_only" falsevalue="" checked="false" label="Only clip E coli insertion elements" />
       <param argument="-is_clip" type="boolean" truevalue="-is_clip" falsevalue="" checked="false" label="Clip IS elements before analysis" help="Normally RepeatMasker will report on IS element, with this option selected it will clip them before analysis" />
@@ -150,7 +151,6 @@
       <param name="xout" type="boolean" argument="-x" truevalue="-x" falsevalue="" checked="false" label="Mask with X instead of N characters" />
       <param name="keep_alignments" type="boolean" argument="-ali" truevalue="-ali" falsevalue="" checked="false" label="Output alignments file" />
       <param name="invert_alignments" type="boolean" argument="-inv" truevalue="-inv" falsevalue="" checked="false" label="Invert alignments in alignment file" help="Show alignments in the orientation of the repeat sequence, not the query sequence" />
-      <param type="boolean" argument="-xsmall" truevalue="-xsmall" falsevalue="" checked="false" label="Output repetitive regions as lowercase, non-repetitive regions as uppercase" />
       <param type="boolean" argument="-poly" truevalue="-poly" falsevalue="" checked="false" label="Output list of potentially polymorphic microsatellites" />
     </section>
   </inputs>