Mercurial > repos > petr-novak > repeat_annotation_pipeline3
comparison extract_re_contigs.xml @ 5:eca9213923b1 draft
"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[ |