# HG changeset patch
# User petr-novak
# Date 1633587078 0
# Node ID a084343c7cc1bc2214e27c5297ae9cde5f47448d
# Parent  cf3cea0a303905ab6b299588845dff26248c70c3
Deleted selected files

diff -r cf3cea0a3039 -r a084343c7cc1 extract_re_contigs2.xml
--- a/extract_re_contigs2.xml	Thu Oct 07 06:07:34 2021 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,20 +0,0 @@
-<tool id="extract_re_contigs2" name="Extract Repeat Library from RepeatExplorer Archive" version="0.1.0" 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'
-    ]]></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" />
-    </inputs>
-    <outputs>
-        <data name="contigs" format="fasta" label="Contigs(Repeat library) extracted from RepeatExplorer archive ${re_archive.hid}"/>
-    </outputs>
-    <help><![CDATA[
-        This tool extracts contigs and TAREAN concesus from RepeatExplorer archive in fasta format. Sequences with reads depth smaller that threshold are removed. Contigs shorter that specied threshold ere also filtered  out. Filtering does not affect TAREAN consensus. Extracted sequences have Id in format CLXContigY where X is cluster ID and Y is number of contig. 
-    ]]></help>
-</tool>
-