Mercurial > repos > petr-novak > re_utils
annotate extract_contigs_from_archive.xml @ 34:91996b991991 draft default tip
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author | petr-novak |
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date | Fri, 16 Feb 2024 15:22:21 +0000 |
parents | 93595f42a04d |
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rev | line source |
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34 | 1 <tool id="extract_contigs" name="Extract contigs from RepeatExplorer2 archive" version="1.0.0.3"> |
1 | 2 <command detect_errors="exit_code"> |
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3 <![CDATA[ |
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4 unzip -p ${RepeatExplorer_archive} contigs.fasta > ${contigs} |
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5 && |
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6 mkdir -p tempdir |
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7 && |
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8 unzip ${RepeatExplorer_archive} "*.aln" -d tempdir |
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9 && |
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10 find tempdir -type f -name "*.aln" -exec cat {} + > ${aln} |
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11 && |
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12 rm -r tempdir |
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13 ]]> |
1 | 14 </command> |
15 | |
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16 |
1 | 17 <inputs> |
18 <param name="RepeatExplorer_archive" label="Archive with RepeatExplorer2 results" type="data" format="zip"/> | |
19 </inputs> | |
20 | |
21 <outputs> | |
9 | 22 <data name="contigs" format="fasta" label="Contigs from RepeatExplorer clustering from data ${RepeatExplorer_archive.hid}" /> |
23 <data name="aln" format="txt" label="Contigs from RepeatExplorer clustering in aln format from data ${RepeatExplorer_archive.hid}" /> | |
1 | 24 </outputs> |
34 | 25 </tool> |