Mercurial > repos > petr-novak > re_utils

comparison extract_contigs_from_archive.xml @ 25:5dba804e6884 draft

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planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
author petr-novak
date Wed, 02 Aug 2023 12:42:08 +0000
parents b50db133106a
children 93595f42a04d
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24:b50db133106a 25:5dba804e6884
1 <tooll id="extract_contigs" name="Extract contigs from RepeatExplorer2 archive" version="1.0.0.3"> 1 <tooll id="extract_contigs" name="Extract contigs from RepeatExplorer2 archive" version="1.0.0.3">
2 <command detect_errors="exit_code"> 2 <command detect_errors="exit_code">
3 <![CDATA[ 3 <![CDATA[
4 unzip -p ${RepeatExplorer_archive} contigs.fasta > ${contigs} 4 unzip -p ${RepeatExplorer_archive} contigs.fasta > ${contigs}
5 && 5 &&
6 mkdir -p tempdir
6 unzip ${RepeatExplorer_archive} "*.aln" -d tempdir 7 unzip ${RepeatExplorer_archive} "*.aln" -d tempdir
7 && 8 &&
8 find tempdir -type f -name "*.aln" -exec cat {} + > ${aln} 9 find tempdir -type f -name "*.aln" -exec cat {} + > ${aln}
9 && 10 &&
10 rm -r tempdir 11 rm -r tempdir