Mercurial > repos > petr-novak > repeat_annotation_pipeline3

annotate extract_re_contigs.xml @ 8:2557cad81607 draft

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author petr-novak
date Wed, 03 May 2023 11:12:41 +0000
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eca9213923b1 "planemo upload commit d13521cdda334d0ce44b9a2bff047168a8bbaae0"
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1 <tool id="extract_re_contigs" name="Extract Repeat Library from RepeatExplorer Archive" version="0.1.1" python_template_version="3.5">
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2 <requirements>
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3 <requirement type="package" version="3">python</requirement>
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4 </requirements>
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5 <command detect_errors="exit_code"><![CDATA[
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eca9213923b1 "planemo upload commit d13521cdda334d0ce44b9a2bff047168a8bbaae0"
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6 $__tool_directory__/get_contigs_from_re_archive.py -re '$re_archive' -m '$min_coverage' -L '$min_length' -f '$contigs'
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7 ]]></command>
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8 <inputs>
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9 <param type="data" name="re_archive" format="zip" label="RepeatExplorer archive"/>
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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"/>
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11 <param type="integer" name="min_length" value="50" min="10" lebel="Minimum length of extracted contigs" />
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12 </inputs>
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13 <outputs>
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14 <data name="contigs" format="fasta" label="Contigs(Repeat library) extracted from RepeatExplorer archive ${re_archive.hid}"/>
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15 </outputs>
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16 <help><![CDATA[
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17 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.
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18 ]]></help>
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19 </tool>
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