--- a/takeabreak.xml	Thu May 06 12:46:24 2021 +0000
+++ b/takeabreak.xml	Sat Oct 05 19:54:32 2024 +0000
@@ -1,10 +1,11 @@
-<tool id="takeabreak" name="TakeABreak" version="1.1.2+galaxy0" profile="@PROFILE@">
+<tool id="takeabreak" name="TakeABreak" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
     <description>is a tool that can detect inversion breakpoints directly from raw NGS reads</description>
     <macros>
+        <token name="@TOOL_VERSION@">1.1.2</token>
         <import>macros.xml</import>
     </macros>
     <requirements>
-        <requirement type="package" version="1.1.2">takeabreak</requirement>
+        <requirement type="package" version="@TOOL_VERSION@">takeabreak</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         #if str($input_type_option.input_type) == "simple"
@@ -46,20 +47,20 @@
                 </repeat>
             </when>
         </conditional>
-        <param name="kmer_size" argument="-kmer-size" type="integer" label="Length of the k-mers" value="31" help="Set the length of used kmers" />
-        <param name="abundance_min" argument="-abundance-min" type="text" label="Minimal abundance threshold" value="auto" />
-        <param name="abundance_max" argument="-abundance-max" type="integer" label="Maximal abundance threshold" value="2147483647" />
-        <param name="solidity_kind" argument="-solidity-kind" type="select" label="Way to consider a solid kmer with several input datasets" >
+        <param argument="-kmer-size" type="integer" label="Length of the k-mers" value="31" help="Set the length of used kmers" />
+        <param argument="-abundance-min" type="text" label="Minimal abundance threshold" value="auto" />
+        <param argument="-abundance-max" type="integer" label="Maximal abundance threshold" value="2147483647" />
+        <param argument="-solidity-kind" type="select" label="Way to consider a solid kmer with several input datasets" >
             <option value="one">One</option>
             <option value="sum">Sum</option>
             <option value="all">All</option>
         </param>
         <param argument="-lct" type="integer" label="local complexity threshold" value="100" help="Local complexity threshold" />
-        <param name="max_sim" argument="-max-sim" type="integer" label="max similarity percentage" value="80" help="Inversions with a and b' (or u and v') whose longest common subsequence size is bigger than k*(this value)/100 are discarded" />
+        <param argument="-max-sim" type="integer" label="max similarity percentage" value="80" help="Inversions with a and b' (or u and v') whose longest common subsequence size is bigger than k*(this value)/100 are discarded" />
         <param argument="-repeat" type="integer" label="maximal repeat size" value="8" help="Maximal repeat size at the breakpoint. Longest common suffix between a and b" />
     </inputs>
     <outputs>
-        <data format="fasta" name="inversion" from_work_dir="TakeABreak_*.fasta" label="Inversions with ${tool.name} on ${on_string}"/>
+        <data format="fasta" name="inversion" from_work_dir="TakeABreak_*.fasta" label="${tool.name} on ${on_string}: Inversions"/>
     </outputs>
     <tests>
         <test>