Mercurial > repos > dfornika > kraken2

changeset 12:269ea4b78bbb draft default tip

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planemo upload for repository https://github.com/dfornika/galaxytools/blob/master/tools/kraken2 commit 70494d589aa1990618ebc7a895e91477d41c3203-dirty
author dfornika
date Mon, 04 Mar 2019 20:22:06 -0500
parents da1a2d98dab1
children
files kraken2.xml macros.xml
diffstat 2 files changed, 1 insertions(+), 3 deletions(-) [+]
line wrap: on
line diff
--- a/kraken2.xml	Mon Mar 04 17:29:41 2019 -0500
+++ b/kraken2.xml	Mon Mar 04 20:22:06 2019 -0500
@@ -9,10 +9,9 @@
     <version_command>kraken2 --version</version_command>
     <command detect_errors="exit_code">
         <![CDATA[
-        @SET_DATABASE_PATH@ &&
         kraken2
             --threads \${GALAXY_SLOTS:-1}
-	    --db '$kraken2_database'
+	    --db '${kraken2_database.fields.path}'
             #if $single_paired.single_paired_selector == 'yes'
                 '${single_paired.forward_input}' '${single_paired.reverse_input}'
             #elif $single_paired.single_paired_selector == "collection":
--- a/macros.xml	Mon Mar 04 17:29:41 2019 -0500
+++ b/macros.xml	Mon Mar 04 20:22:06 2019 -0500
@@ -15,5 +15,4 @@
             <citation type="doi">10.1186/gb-2014-15-3-r46</citation>
         </citations>
     </xml>
-    <token name="@SET_DATABASE_PATH@">export KRAKEN2_DB_PATH='${kraken2_database.fields.path}'</token>
 </macros>