--- a/repeat_annotate_custom.xml	Thu May 04 09:27:43 2023 +0000
+++ b/repeat_annotate_custom.xml	Fri Aug 04 12:35:32 2023 +0000
@@ -1,8 +1,11 @@
-<tool id="repeat_annotate" name="Library Based Assembly Annotation" version="0.1.5" python_template_version="3.5">
+<tool id="repeat_annotate" name="Library Based Assembly Annotation" version="0.1.6" python_template_version="3.5">
     <requirements>
         <requirement type="package" version="4.1.2.p1">repeatmasker</requirement>
         <requirement type="package">bioconductor-rtracklayer</requirement>
     </requirements>
+    <required_files>
+        <include type="literal" path="clean_rm_output.R"/>
+    </required_files>
     <command detect_errors="exit_code"><![CDATA[
 
         #if $sensitivity.value == 'default':
@@ -27,7 +30,7 @@
             <option value="-s">Slow search, more sensitive </option>
             <option value="-q">Quick search, less sensitive </option>
         </param>
-        <param argument="-nolow" type="boolean" truevalue="-nolow" falsevalue="" checked="false" label="Perform masking of low complexity and simple repeats" />
+        <param argument="-nolow" type="boolean" truevalue="" falsevalue="-nolow" checked="false" label="Perform masking of low complexity and simple repeats" />
     </inputs>
     <outputs>
         <data name="output1" format="gff3"  label="Repeat Annotation (GFF3) on ${on_string}"/>