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comparison extract_contigs_from_archive.xml @ 24:b50db133106a draft

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planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty
author petr-novak
date Wed, 02 Aug 2023 12:28:39 +0000
parents 36c418bca8b2
children 5dba804e6884
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23:36c418bca8b2 24:b50db133106a
1 <tool 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 unzip -p ${RepeatExplorer_archive} contigs.fasta &gt; ${contigs} 3 <![CDATA[
4 &amp;&amp; 4 unzip -p ${RepeatExplorer_archive} contigs.fasta > ${contigs}
5 unzip -p -j ${RepeatExplorer_archive} "*.aln" &gt; ${aln} 5 &&
6 unzip ${RepeatExplorer_archive} "*.aln" -d tempdir
7 &&
8 find tempdir -type f -name "*.aln" -exec cat {} + > ${aln}
9 &&
10 rm -r tempdir
11 ]]>
6 </command> 12 </command>
13
7 14
8 <inputs> 15 <inputs>
9 <param name="RepeatExplorer_archive" label="Archive with RepeatExplorer2 results" type="data" format="zip"/> 16 <param name="RepeatExplorer_archive" label="Archive with RepeatExplorer2 results" type="data" format="zip"/>
10 </inputs> 17 </inputs>
11 18
12 <outputs> 19 <outputs>
13 <data name="contigs" format="fasta" label="Contigs from RepeatExplorer clustering from data ${RepeatExplorer_archive.hid}" /> 20 <data name="contigs" format="fasta" label="Contigs from RepeatExplorer clustering from data ${RepeatExplorer_archive.hid}" />
14 <data name="aln" format="txt" label="Contigs from RepeatExplorer clustering in aln format from data ${RepeatExplorer_archive.hid}" /> 21 <data name="aln" format="txt" label="Contigs from RepeatExplorer clustering in aln format from data ${RepeatExplorer_archive.hid}" />
15 </outputs> 22 </outputs>
16 </tool> 23 </tooll>