Mercurial > repos > iuc > drep_dereplicate

comparison drep_dereplicate.xml @ 7:c55eec39f086 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 620124793ed18545728d07cfd8592065bc5c6c2d
author iuc
date Fri, 21 Mar 2025 07:04:02 +0000
parents 055649d1378e
children caaf7cbaafbf
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6:055649d1378e 7:c55eec39f086
6 <expand macro="biotools" /> 6 <expand macro="biotools" />
7 <expand macro="requirements"> 7 <expand macro="requirements">
8 <requirement type="package" version="1.2.2">checkm-genome</requirement> 8 <requirement type="package" version="1.2.2">checkm-genome</requirement>
9 </expand> 9 </expand>
10 <command detect_errors="exit_code"><![CDATA[ 10 <command detect_errors="exit_code"><![CDATA[
11 @PREPARE_GENOMES@ 11 @PREPARE_GENOMES@
12 dRep dereplicate outdir 12 dRep
13 @GENOMES@ 13 dereplicate
14 @FILTER_OPTIONS@ 14 outdir
15 @QUALITY_ASSESSMENT_OPTIONS@ 15 @GENOMES@
16 @COMPARISON_CLUSTERING_OPTIONS@ 16 @FILTER_OPTIONS@
17 @SCORING_OPTIONS@ 17 @QUALITY_ASSESSMENT_OPTIONS@
18 @WARNING_OPTIONS@ 18 @COMPARISON_CLUSTERING_OPTIONS@
19 --debug 19 @SCORING_OPTIONS@
20 @WARNING_OPTIONS@
21 --processors \${GALAXY_SLOTS:-1}
20 || (rc=\$?; 22 || (rc=\$?;
21 ls -ltr `find outdir -type f`; 23 ls -ltr `find outdir -type f`;
22 cat outdir/data/checkM/checkM_outdir/checkm.log; 24 cat outdir/data/checkM/checkM_outdir/checkm.log;
23 cat outdir/log/logger.log; 25 cat outdir/log/logger.log;
24 exit \$rc) 26 exit \$rc)