Mercurial > repos > petr-novak > dante_ltr
comparison dante_ltr_to_library.xml @ 17:d1c3b29b1478 draft
planemo upload commit ce025ba66edc87ff8ced32d5fdb36109f12cebf0-dirty
| author | petr-novak |
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| date | Thu, 10 Aug 2023 12:22:28 +0000 |
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| 16:7ec262f92d89 | 17:d1c3b29b1478 |
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| 1 <tool id="dante_ltr_to_library" name="Create representative library from DANTE_LTR output " version="@TOOL_VERSION@" python_template_version="3.5"> | |
| 2 <macros> | |
| 3 <import>macros.xml</import> | |
| 4 </macros> | |
| 5 <expand macro="requirements" /> | |
| 6 <command detect_errors="exit_code"><![CDATA[ | |
| 7 cp '$dante_ltr' dante_ltr.gff3 && | |
| 8 dante_ltr_to_library --gff3 dante_ltr.gff3 --reference_sequence '$reference' --output output --cpu \${GALAXY_SLOTS:-1} --min_coverage 3 | |
| 9 && | |
| 10 ls -l output | |
| 11 && | |
| 12 mv output/mmseqs2/mmseqs_representative_seq_clean.fasta $dante_ltr_library | |
| 13 ]]></command> | |
| 14 <inputs> | |
| 15 <param type="data" name="dante_ltr" format="gff3" | |
| 16 label="GFF3 output from DANTE_LTR retrotransposon identification pipeline"/> | |
| 17 <param type="data" name="reference" format="fasta" label="Reference sequence matching input GFF3" /> | |
| 18 </inputs> | |
| 19 <outputs> | |
| 20 <data name="dante_ltr_library" format="fasta" | |
| 21 label="Representative library from DANTE_LTR $dante_ltr.hid on reference $reference.hid"/> | |
| 22 </outputs> | |
| 23 <help><![CDATA[ | |
| 24 This tool extract representative sequences from LTR-RT library identified | |
| 25 by DANTE_LTR. Resulting library is suitable for RepeatMasker search. | |
| 26 ]]></help> | |
| 27 </tool> | |
| 28 |