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comparison extract_contigs_from_archive.xml @ 2:ff658cf87f16 draft

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author petr-novak
date Wed, 04 Sep 2019 07:33:42 -0400
parents 2e811f988e1d
children c2c69c6090f0
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1:2e811f988e1d 2:ff658cf87f16
1 <tool id="extract_contigs" name="Extract contigs from RepeatExplorer2 archive"> 1 <tool id="extract_contigs" name="Extract contigs from RepeatExplorer2 archive">
2 <command detect_errors="exit_code"> 2 <command detect_errors="exit_code">
3 unzip -p ${RepeatExplorer_archive} contigs.fasta &gt; ${contigs} 3 unzip -p ${RepeatExplorer_archive} contigs.fasta &gt; ${contigs}
4 &amp;&amp;
5 unzip -p -j ${RepeatExplorer_archive} "*.aln" &gt; ${aln}
4 </command> 6 </command>
5 7
6 <inputs> 8 <inputs>
7 <param name="RepeatExplorer_archive" label="Archive with RepeatExplorer2 results" type="data" format="zip"/> 9 <param name="RepeatExplorer_archive" label="Archive with RepeatExplorer2 results" type="data" format="zip"/>
8 </inputs> 10 </inputs>
9 11
10 <outputs> 12 <outputs>
11 <data name="contigs" format="fasta" label="contigs from RepeatExplorer clustering - data ${RepeatExplorer_archive.hid}" /> 13 <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}" />
12 </outputs> 15 </outputs>
13 </tool> 16 </tool>