Mercurial > repos > petr-novak > repeat_annotation_pipeline3

comparison extract_re_contigs.xml @ 11:5366d5ea04bc draft

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planemo upload commit 9d1b19f98d8b7f0a0d1baf2da63a373d155626f8-dirty
author petr-novak
date Fri, 04 Aug 2023 12:35:32 +0000
parents eca9213923b1
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10:276efc4cb17f 11:5366d5ea04bc
1 <tool id="extract_re_contigs" name="Extract Repeat Library from RepeatExplorer Archive" version="0.1.1" 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 <required_files>
6 <include type="literal" path="get_contigs_from_re_archive.py"/>
7 </required_files>
5 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
6 $__tool_directory__/get_contigs_from_re_archive.py -re '$re_archive' -m '$min_coverage' -L '$min_length' -f '$contigs' 9 python $__tool_directory__/get_contigs_from_re_archive.py -re '$re_archive' -m '$min_coverage' -L '$min_length' -f '$contigs'
7 ]]></command> 10 ]]></command>
8 <inputs> 11 <inputs>
9 <param type="data" name="re_archive" format="zip" label="RepeatExplorer archive"/> 12 <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"/> 13 <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="50" min="10" lebel="Minimum length of extracted contigs" /> 14 <param type="integer" name="min_length" value="50" min="10" lebel="Minimum length of extracted contigs" />