Mercurial > repos > petr-novak > repeat_annotation_pipeline3

view extract_re_contigs.xml @ 6:b53f5a456d01 draft

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"planemo upload commit 3aefb0555456837d10fe69e4ad25de08d5972cb2"
author petr-novak
date Thu, 19 May 2022 08:23:55 +0000
parents eca9213923b1
children 5366d5ea04bc
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<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 '$min_coverage' -L '$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="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}"/>
    </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>