Mercurial > repos > petr-novak > repeat_annotation_pipeline3

comparison extract_re_contigs.xml @ 5:eca9213923b1 draft

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"planemo upload commit d13521cdda334d0ce44b9a2bff047168a8bbaae0"
author petr-novak
date Fri, 22 Apr 2022 10:26:11 +0000
parents ea6a3059a6af
children 5366d5ea04bc
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4:d7bb42f254a2 5:eca9213923b1
1 <tool id="extract_re_contigs" name="Extract Repeat Library from RepeatExplorer Archive" version="0.1.0" python_template_version="3.5"> 1 <tool id="extract_re_contigs" name="Extract Repeat Library from RepeatExplorer Archive" version="0.1.1" python_template_version="3.5">
2 <requirements> 2 <requirements>
3 <requirement type="package" version="3">python</requirement> 3 <requirement type="package" version="3">python</requirement>
4 </requirements> 4 </requirements>
5 <command detect_errors="exit_code"><![CDATA[ 5 <command detect_errors="exit_code"><![CDATA[
6 $__tool_directory__/get_contigs_from_re_archive.py -re '$re_archive' -m 5 -L 50 -f '$contigs' 6 $__tool_directory__/get_contigs_from_re_archive.py -re '$re_archive' -m '$min_coverage' -L '$min_length' -f '$contigs'
7 ]]></command> 7 ]]></command>
8 <inputs> 8 <inputs>
9 <param type="data" name="re_archive" format="zip" label="RepeatExplorer archive"/> 9 <param type="data" name="re_archive" format="zip" label="RepeatExplorer archive"/>
10 <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"/> 10 <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"/>
11 <param type="integer" name="min_length" value="20" min="10" lebel="Minimum length of extracted contigs" /> 11 <param type="integer" name="min_length" value="50" min="10" lebel="Minimum length of extracted contigs" />
12 </inputs> 12 </inputs>
13 <outputs> 13 <outputs>
14 <data name="contigs" format="fasta" label="Contigs(Repeat library) extracted from RepeatExplorer archive ${re_archive.hid}"/> 14 <data name="contigs" format="fasta" label="Contigs(Repeat library) extracted from RepeatExplorer archive ${re_archive.hid}"/>
15 </outputs> 15 </outputs>
16 <help><![CDATA[ 16 <help><![CDATA[