Mercurial > repos > iuc > data_manager_build_bracken_database

changeset 1:9059edc96a85 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 2e8d990fa8b6de085046195464071020b467ce5a"
author iuc
date Sun, 19 Jan 2020 04:33:53 -0500
parents c2e4127fb5bf
children fd5830f88314
files data_manager/bracken_build_database.xml test-data/bracken_databases.loc tool_data_table_conf.xml.test
diffstat 2 files changed, 11 insertions(+), 1 deletions(-) [+]
line wrap: on
line diff
--- a/data_manager/bracken_build_database.xml	Sun Oct 20 09:37:21 2019 -0400
+++ b/data_manager/bracken_build_database.xml	Sun Jan 19 04:33:53 2020 -0500
@@ -7,9 +7,14 @@
     </requirements>
     <command>
     <![CDATA[
+        #import os
+        #set db_dir = os.path.basename($kraken_db.fields.path)
+
+        mkdir '$db_dir' &&
+        ln -s '${kraken_db.fields.path}'/* '$db_dir/' &&
         python '$__tool_directory__/bracken_build_database.py'
           '${out_file}'
-          --kraken-db '${kraken_db.fields.path}'
+          --kraken-db '$db_dir'
           --threads \${GALAXY_SLOTS:-1}
           --kmer-len ${kmer_len}
           --read-len ${read_len}
--- a/tool_data_table_conf.xml.test	Sun Oct 20 09:37:21 2019 -0400
+++ b/tool_data_table_conf.xml.test	Sun Jan 19 04:33:53 2020 -0500
@@ -5,4 +5,9 @@
         <columns>value, name, path</columns>
         <file path="${__HERE__}/test-data/kraken2_databases.loc" />
     </table>
+    <!-- Locations of bracken databases in the required format -->
+    <table name="bracken_databases" comment_char="#">
+        <columns>value, name, path</columns>
+        <file path="${__HERE__}/test-data/bracken_databases.loc" />
+    </table>
 </tables>