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annotate dante_ltr_to_library.xml @ 17:d1c3b29b1478 draft

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author petr-novak
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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