Mercurial > repos > petr-novak > re_utils
changeset 24:b50db133106a draft
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
| author | petr-novak |
|---|---|
| date | Wed, 02 Aug 2023 12:28:39 +0000 |
| parents | 36c418bca8b2 |
| children | 5dba804e6884 |
| files | extract_contigs_from_archive.xml |
| diffstat | 1 files changed, 12 insertions(+), 5 deletions(-) [+] |
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--- a/extract_contigs_from_archive.xml Wed Aug 02 11:50:25 2023 +0000 +++ b/extract_contigs_from_archive.xml Wed Aug 02 12:28:39 2023 +0000 @@ -1,10 +1,17 @@ -<tool id="extract_contigs" name="Extract contigs from RepeatExplorer2 archive" version="1.0.0.3"> +<tooll id="extract_contigs" name="Extract contigs from RepeatExplorer2 archive" version="1.0.0.3"> <command detect_errors="exit_code"> - unzip -p ${RepeatExplorer_archive} contigs.fasta > ${contigs} - && - unzip -p -j ${RepeatExplorer_archive} "*.aln" > ${aln} + <![CDATA[ + unzip -p ${RepeatExplorer_archive} contigs.fasta > ${contigs} + && + unzip ${RepeatExplorer_archive} "*.aln" -d tempdir + && + find tempdir -type f -name "*.aln" -exec cat {} + > ${aln} + && + rm -r tempdir + ]]> </command> + <inputs> <param name="RepeatExplorer_archive" label="Archive with RepeatExplorer2 results" type="data" format="zip"/> </inputs> @@ -13,4 +20,4 @@ <data name="contigs" format="fasta" label="Contigs from RepeatExplorer clustering from data ${RepeatExplorer_archive.hid}" /> <data name="aln" format="txt" label="Contigs from RepeatExplorer clustering in aln format from data ${RepeatExplorer_archive.hid}" /> </outputs> -</tool> +</tooll>