# HG changeset patch
# User petr-novak
# Date 1650623171 0
# Node ID eca9213923b100e3361ff85b9e87e05dc9abccf4
# Parent  d7bb42f254a29e5b4c8505ca5da80f843e3d24fc
"planemo upload commit d13521cdda334d0ce44b9a2bff047168a8bbaae0"

diff -r d7bb42f254a2 -r eca9213923b1 extract_re_contigs.xml
--- a/extract_re_contigs.xml	Mon Mar 14 10:16:07 2022 +0000
+++ b/extract_re_contigs.xml	Fri Apr 22 10:26:11 2022 +0000
@@ -1,14 +1,14 @@
-<tool id="extract_re_contigs" name="Extract Repeat Library from RepeatExplorer Archive" version="0.1.0" python_template_version="3.5">
+<tool id="extract_re_contigs" name="Extract Repeat Library from RepeatExplorer Archive" version="0.1.1" python_template_version="3.5">
     <requirements>
         <requirement type="package" version="3">python</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
-        $__tool_directory__/get_contigs_from_re_archive.py -re '$re_archive' -m 5 -L 50 -f '$contigs'
+        $__tool_directory__/get_contigs_from_re_archive.py -re '$re_archive' -m '$min_coverage' -L '$min_length' -f '$contigs'
     ]]></command>
     <inputs>
         <param type="data" name="re_archive" format="zip" label="RepeatExplorer archive"/>
         <param type="integer" name="min_coverage" value="5" min="1" max="100" label="minimal read depth coverage of contigs" help="region with lower coverage are trimmed off or hardmasked"/>
-        <param type="integer" name="min_length" value="20" min="10" lebel="Minimum length of extracted contigs" />
+        <param type="integer" name="min_length" value="50" min="10" lebel="Minimum length of extracted contigs" />
     </inputs>
     <outputs>
         <data name="contigs" format="fasta" label="Contigs(Repeat library) extracted from RepeatExplorer archive ${re_archive.hid}"/>