Mercurial > repos > iuc > drep_dereplicate

diff drep_dereplicate.xml @ 7:c55eec39f086 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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
line wrap: on
line diff
--- a/drep_dereplicate.xml	Mon Jan 13 12:44:25 2025 +0000
+++ b/drep_dereplicate.xml	Fri Mar 21 07:04:02 2025 +0000
@@ -8,15 +8,17 @@
         <requirement type="package" version="1.2.2">checkm-genome</requirement>
     </expand>
     <command detect_errors="exit_code"><![CDATA[
-@PREPARE_GENOMES@
-dRep dereplicate outdir
-@GENOMES@
-@FILTER_OPTIONS@
-@QUALITY_ASSESSMENT_OPTIONS@
-@COMPARISON_CLUSTERING_OPTIONS@
-@SCORING_OPTIONS@
-@WARNING_OPTIONS@
---debug
+    @PREPARE_GENOMES@
+    dRep
+        dereplicate 
+        outdir
+        @GENOMES@
+        @FILTER_OPTIONS@
+        @QUALITY_ASSESSMENT_OPTIONS@
+        @COMPARISON_CLUSTERING_OPTIONS@
+        @SCORING_OPTIONS@
+        @WARNING_OPTIONS@
+        --processors \${GALAXY_SLOTS:-1}
 || (rc=\$?;
     ls -ltr `find outdir -type f`;
     cat outdir/data/checkM/checkM_outdir/checkm.log;