--- a/integron_finder.xml	Fri Feb 17 18:35:52 2023 +0000
+++ b/integron_finder.xml	Tue Feb 10 15:53:43 2026 +0000
@@ -1,5 +1,5 @@
 <tool id="integron_finder" name="Integron Finder" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
-    <description> is a program that detects integrons in DNA sequences</description>
+    <description>is a program that detects integrons in DNA sequences</description>
     <macros>
        <import>macro.xml</import>
     </macros>
@@ -38,43 +38,43 @@
         <param type="data" name="sequence" format="fasta" label="Replicon file" help="Replicon can be entire chromosome, contif, PCR fragments...">
              <validator type="expression" message="Integron Finder has problems with large multi FASTA files. Please assembly your sequences or split them up into files smaller 10.000 sequences."><![CDATA[value is not None and value.metadata.sequences <= 10000]]></validator>
         </param>
-        <param name="local_max" argument="--local-max" type="boolean" checked="false" truevalue="--local-max" falsevalue="" label="Thorough local detection" help="This option allows a more sensitive search. I will be slower (dependant on the number of hits) if integrons are found, but will be as fast if nothing is detected and will not increase the false positive rate." />
+        <param argument="--local-max" type="boolean" checked="false" truevalue="--local-max" falsevalue="" label="Thorough local detection" help="This option allows a more sensitive search. I will be slower (dependant on the number of hits) if integrons are found, but will be as fast if nothing is detected and will not increase the false positive rate." />
 	      <param name="type_replicon" type="select" optional="true" label="Default replicons topology" help="Set the default topology for replicons, linear, circular (deault: no topology)">
 	          <option value="--linear">linear (--linear)</option>
 	          <option value="--circ">circular (--circ)</option>
 	      </param>
-        <param name="topology_file" argument="--topology-file" type="data" format="txt" optional="true" label="Select a topology file from your history"/>
-        <param name="promoter_attI" argument="--promoter-attI" type="boolean" checked="false" truevalue="--promoter-attI" falsevalue="" label="Search also for promoter and attI sites?" />
+        <param argument="--topology-file" type="data" format="txt" optional="true" label="Select a topology file from your history"/>
+        <param argument="--promoter-attI" type="boolean" checked="false" truevalue="--promoter-attI" falsevalue="" label="Search also for promoter and attI sites?" />
         <param argument="--gbk" type="boolean" checked="false" truevalue="--gbk" falsevalue="" label="Genbank output?" help="Generate a GenBank file with the sequence annotated with the same annotations than .integrons file."/>
-        <param argument="--pdf" type="boolean" checked="false" truevalue="--pdf" falsevalue="" label="pdf output?" help="For each complete integron, a simple graphic of the region is depicted (in pdf format)"/>
+        <param argument="--pdf" type="boolean" checked="false" truevalue="--pdf" falsevalue="" label="PDF output?" help="For each complete integron, a simple graphic of the region is depicted (in pdf format)"/>
         <section name="settings" title="Advanced Parameters" expanded="False">
             <section name="attc_settings" title="Attc options" expanded="False">
                <param name="dist_thresh" argument="--distance-thresh" type="integer" value="4000" label="Threshold for clustering (in base)" min="0" help="By default, to cluster an array of attC sites and an integron integrase, they must be less than 4 kb apart. You can here change this value." />
                <param name="calin_threshold" type="integer" value="2" label="Threshold to filter CALIN" min="0" help="Keep 'CALIN' only if attC sites number >= calin-threshold" />
                <param name="max_attc_size" type="integer" value="200" label="Maximum value for attC size" min="0"/>
                <param name="min_attc_size" type="integer" value="40" label="Minimum value for attC size" min="0" />
-               <param name="keep_palindromes" argument="--keep-palindromes" type="boolean" checked="false" truevalue="--keep-palindromes" falsevalue="" label="Keep palindromes with the highest evalue" help="For a given hit, if the palindromic version is found, don't remove the one with highest evalue"/>
+               <param argument="--keep-palindromes" type="boolean" checked="false" truevalue="--keep-palindromes" falsevalue="" label="Keep palindromes with the highest evalue" help="For a given hit, if the palindromic version is found, don't remove the one with highest evalue"/>
                <param name="covar_matrix" argument="--attc-model" type="data"  optional="true" format="txt" label="Covariance Matrix" />
             </section>
             <section name="protein_settings" title="Protein options" expanded="False">
-                <param name="no_proteins" argument="--no-proteins" type="boolean" checked="false" truevalue="--no-proteins" falsevalue="" label="Just look for attC sites" help="When enabled, it does not annotate CDS and does not find integrase."/>
-                <param name="union_integrases" argument="--union-integrases" type="boolean" checked="false" truevalue="--union-integrases" falsevalue="" label="Use the union of the hits" help="Instead of taking intersection of hits from Phage_int profile (Tyr recombinases) and integron_integrase profile, use the union of the hits" />
-                <param name="func_annot" argument="--func-annot" type="boolean" checked="false" truevalue="--func-annot" falsevalue="" label="Annotate cassettes given HMM profiles" />
+                <param argument="--no-proteins" type="boolean" checked="false" truevalue="--no-proteins" falsevalue="" label="Just look for attC sites" help="When enabled, it does not annotate CDS and does not find integrase."/>
+                <param argument="--union-integrases" type="boolean" checked="false" truevalue="--union-integrases" falsevalue="" label="Use the union of the hits" help="Instead of taking intersection of hits from Phage_int profile (Tyr recombinases) and integron_integrase profile, use the union of the hits" />
+                <param argument="--func-annot" type="boolean" checked="false" truevalue="--func-annot" falsevalue="" label="Annotate cassettes given HMM profiles" />
             </section>
         </section>
         <param name="no_logfile" type="boolean" truevalue="true" falsevalue="false" label="Remove log file"/>
     </inputs>
     <outputs>
-        <collection type="list" label="Genbank files from [$tool.name] on $[on_string]" name="genbank_out">
-            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.gbk" format="gbk" visible="false" directory="Results_Integron_Finder/" />
+        <collection type="list" label="${tool.name} on ${on_string}: Genbank " name="genbank_out">
+            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.gbk" format="genbank" visible="false" directory="Results_Integron_Finder/" />
             <filter>gbk</filter>
         </collection>
-	      <data format="txt" name="integron_log" from_work_dir="Results_Integron_Finder/integron_finder.out" label="Log from [$tool.name] on $[on_string]">
+	    <data format="txt" name="integron_log" from_work_dir="Results_Integron_Finder/integron_finder.out" label="${tool.name} on ${on_string}: Log">
             <filter> no_logfile == False</filter>
         </data>
-        <data format="tsv" name="integrons_table" from_work_dir="Results_Integron_Finder/*.integrons" label="Integrons annotations from [$tool.name] on $[on_string]"/>
-        <data format="tsv" name="summary" from_work_dir="Results_Integron_Finder/*.summary" label="Summary from [$tool.name] on $[on_string]"/>
-        <collection type="list" label="Graphic from [$tool.name] on $[on_string]" name="pdf_out">
+        <data format="tsv" name="integrons_table" from_work_dir="Results_Integron_Finder/*.integrons" label="${tool.name} on ${on_string}: Integron annotations"/>
+        <data format="tsv" name="summary" from_work_dir="Results_Integron_Finder/*.summary" label="${tool.name} on ${on_string}: Summary"/>
+        <collection name="pdf_out" type="list" label="${tool.name} on ${on_string}: Graphic">
             <discover_datasets pattern="(?P&lt;designation&gt;.+)\.pdf" format="pdf" visible="false" directory="Results_Integron_Finder/" />
             <filter>pdf</filter>
         </collection>
@@ -146,7 +146,7 @@
                     <param name="calin_threshold" value="3"/>
                     <param name="max_attc_size" value="188"/>
                     <param name="min_attc_size" value="30"/>
-                    <param name="keep_palindromes" value=""/>
+                    <param name="keep_palindromes" value="false"/>
                 </section>
             </section>
             <output name="integrons_table" value="test7_integrons_table.tsv" lines_diff="3" />