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annotate extract_contigs_from_archive.xml @ 25:5dba804e6884 draft

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author petr-novak
date Wed, 02 Aug 2023 12:42:08 +0000
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1 <tooll id="extract_contigs" name="Extract contigs from RepeatExplorer2 archive" version="1.0.0.3">
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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 unzip ${RepeatExplorer_archive} "*.aln" -d tempdir
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8 &&
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9 find tempdir -type f -name "*.aln" -exec cat {} + > ${aln}
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10 &&
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11 rm -r tempdir
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12 ]]>
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13 </command>
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16 <inputs>
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17 <param name="RepeatExplorer_archive" label="Archive with RepeatExplorer2 results" type="data" format="zip"/>
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18 </inputs>
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20 <outputs>
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21 <data name="contigs" format="fasta" label="Contigs from RepeatExplorer clustering from data ${RepeatExplorer_archive.hid}" />
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22 <data name="aln" format="txt" label="Contigs from RepeatExplorer clustering in aln format from data ${RepeatExplorer_archive.hid}" />
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23 </outputs>
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24 </tooll>