# HG changeset patch
# User iuc
# Date 1725262863 0
# Node ID 465dcff3b2a7d58d69e1de1b3244f9be09c22ce3
# Parent  9f65d5e29e943abb75b1b67212cf231f6a8855d8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear commit 3efdc8b41f4f54d034d43b833733324153771fcf

diff -r 9f65d5e29e94 -r 465dcff3b2a7 pear.xml
--- a/pear.xml	Mon Aug 12 07:14:53 2024 +0000
+++ b/pear.xml	Mon Sep 02 07:41:03 2024 +0000
@@ -2,7 +2,7 @@
     <description>Paired-End read merger</description>
     <macros>
         <token name="@TOOL_VERSION@">0.9.6</token>
-        <token name="@VERSION_SUFFIX@">3</token>
+        <token name="@VERSION_SUFFIX@">4</token>
         <xml name="format_action">
             <actions>
                 <conditional name="library.type">
@@ -59,10 +59,10 @@
         --quality-theshold $quality_threshold
         --max-uncalled-base $max_uncalled_base
         --test-method $test_method
-        --empirical-freqs $empirical_freqs
         --threads "\${GALAXY_SLOTS:-8}"
         --score-method $score_method
         --cap $cap
+        $empirical_freqs
         $nbase
 ]]>
     </command>
@@ -93,7 +93,7 @@
             <option value="1" selected="true">Given the minimum allowed overlap, test using the highest OES (1)</option>
             <option value="2">Use the acceptance probability (2)</option>
         </param>
-        <param name="empirical_freqs" type="boolean" truevalue="-e" falsevalue="" checked="false" label="Disable empirical base frequencies" help="(--empirical-freqs)"/>
+        <param name="empirical_freqs" type="boolean" truevalue="--empirical-freqs" falsevalue="" checked="false" label="Disable empirical base frequencies" help="(--empirical-freqs)"/>
         <param name="nbase" type="boolean" truevalue="--nbase" falsevalue="" checked="false" label="Use N base if uncertain" help="When  merging a base-pair that consists of two non-equal bases out of which none is degenerate, set the merged base to N and use the highest quality score of the two bases. (--nbase)"/>
         <param name="score_method" type="select" label="Scoring method" help="(--score-method)">
             <option value="1">OES with +1 for match and -1 for mismatch</option>