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author | petr-novak |
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date | Thu, 18 Apr 2024 08:56:19 +0000 |
parents | d1c3b29b1478 |
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<tool id="dante_ltr_to_library" name="Create representative library from DANTE_LTR output " version="@TOOL_VERSION@" python_template_version="3.5"> <macros> <import>macros.xml</import> </macros> <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ cp '$dante_ltr' dante_ltr.gff3 && dante_ltr_to_library --gff3 dante_ltr.gff3 --reference_sequence '$reference' --output output --cpu \${GALAXY_SLOTS:-1} --min_coverage 3 && ls -l output && mv output/mmseqs2/mmseqs_representative_seq_clean.fasta $dante_ltr_library ]]></command> <inputs> <param type="data" name="dante_ltr" format="gff3" label="GFF3 output from DANTE_LTR retrotransposon identification pipeline"/> <param type="data" name="reference" format="fasta" label="Reference sequence matching input GFF3" /> </inputs> <outputs> <data name="dante_ltr_library" format="fasta" label="Representative library from DANTE_LTR $dante_ltr.hid on reference $reference.hid"/> </outputs> <help><![CDATA[ This tool extract representative sequences from LTR-RT library identified by DANTE_LTR. Resulting library is suitable for RepeatMasker search. ]]></help> </tool>