# HG changeset patch
# User iuc
# Date 1728145890 0
# Node ID 8bafa5dad84a99955740c314ca3990d65aa10794
# Parent  571d2bf23290d98bdc1c8fad3742bc53e6e1f0e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gecko commit b55cfca7f53d2eaa3f4c7c4ce09436371b088000

diff -r 571d2bf23290 -r 8bafa5dad84a gecko.xml
--- a/gecko.xml	Mon Jan 04 21:01:30 2021 +0000
+++ b/gecko.xml	Sat Oct 05 16:31:30 2024 +0000
@@ -1,7 +1,8 @@
-<tool id="gecko" name="Gecko" version="@TOOL_VERSION@" profile="20.01">
+<tool id="gecko" name="Gecko" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.1">
     <description>Ungapped genome comparison</description>
     <macros>
         <token name="@TOOL_VERSION@">1.2</token>
+        <token name="@VERSION_SUFFIX@">1</token>
     </macros>
     <requirements>
         <requirement type="package" version="@TOOL_VERSION@">gecko</requirement>
@@ -14,7 +15,7 @@
     cp $db db.fasta &&
     workflow.sh query.fasta db.fasta $minlen $similarity $kmer 1 &&
     rm -rf intermediateFiles &&
-    #if str($options['selection_mode']) == "alignments":
+    #if str($selection_mode) == "alignments":
       frags2align.sh results/query-db.frags query.fasta db.fasta results/query-db.txt &&
       mv results/query-db.txt $alignments2 &&
     #end if
@@ -37,17 +38,15 @@
         </param>
         <param name="minlen" type="integer" value="40" min="8" label="Minimum length" help="The minimum length a fragment must achieve to be reported"/>
         <param name="similarity" type="integer" value="60" min="1" max="99" label="Minimum similarity" help="Percentage of similarity threshold (calculated as the attained score divided by the maximum possible score)"/>
-        <conditional name="options">
-            <param label="Generate alignments file?" name="selection_mode" type="select">
-                <option selected="true" value="noalignments">Do not extract alignments (Only CSV file)</option>
-                <option value="alignments">Extract alignments (CSV and alignments file)</option>
-            </param>
-        </conditional>
+        <param label="Generate alignments file?" name="selection_mode" type="select">
+            <option selected="true" value="noalignments">Do not extract alignments (Only CSV file)</option>
+            <option value="alignments">Extract alignments (CSV and alignments file)</option>
+        </param>
     </inputs>
     <outputs>
         <data name="csv_output1" format="csv" label="${tool.name} on ${on_string}: CSV"/> 
         <data name="alignments2" format="txt" label="${tool.name} on ${on_string}: Alignments">
-            <filter> options['selection_mode'] == 'alignments'</filter>
+            <filter> selection_mode == 'alignments'</filter>
         </data>
     </outputs>
     <tests>