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