# HG changeset patch
# User dfornika
# Date 1564614549 14400
# Node ID cc49eb0defeecba135a01e9645295f16d0222315
# Parent  f25264bb7d6d133b60128715f89c97952f91eb07
planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_bracken_database/ commit 324b55b24e9d403b04a1cc6aba362b03bad98368-dirty

diff -r f25264bb7d6d -r cc49eb0defee data_manager/bracken_build_database.py
--- a/data_manager/bracken_build_database.py	Wed Jul 31 18:08:06 2019 -0400
+++ b/data_manager/bracken_build_database.py	Wed Jul 31 19:09:09 2019 -0400
@@ -25,15 +25,7 @@
 
     database_name = database_name
 
-    database_path = bracken_build_args['kraken_database']
-
-    try:
-        os.mkdir( os.path.join(target_directory, database_path) )
-    except OSError as exc:
-        if exc.errno == errno.EEXIST and os.path.isdir( os.path.join(target_directory, database_path) ):
-            pass
-        else:
-            raise
+    database_path = os.path.join(bracken_build_args['kraken_database'], 'database' + str(bracken_build_args['read_len']) + 'mers.kmer_distrib') 
 
 
     bracken_build_args_list = [
@@ -43,8 +35,7 @@
         '-d', bracken_build_args['kraken_database'],
     ]
 
-    subprocess.check_call(['bracken-build'] + bracken_build_args_list,
-                          cwd=os.path.join(target_directory, database_path))
+    subprocess.check_call(['bracken-build'] + bracken_build_args_list)
 
     
     data_table_entry = {
@@ -53,7 +44,7 @@
                 {
                     "value": database_value,
                     "name": database_name,
-                    "path": os.path.join(database_path),
+                    "path": database_path,
                 }
             ]
         }
diff -r f25264bb7d6d -r cc49eb0defee data_manager/bracken_build_database.xml
--- a/data_manager/bracken_build_database.xml	Wed Jul 31 18:08:06 2019 -0400
+++ b/data_manager/bracken_build_database.xml	Wed Jul 31 19:09:09 2019 -0400
@@ -4,14 +4,13 @@
     <requirements>
         <requirement type="package" version="2.2">bracken</requirement>
         <requirement type="package" version="2.0.8_beta">kraken2</requirement>
-        <requirement type="package" version="1.7.0">bagit</requirement>
     </requirements>
     <version_command>bracken --version</version_command>
     <command detect_errors="exit_code">
     <![CDATA[
         python '$__tool_directory__/bracken_build_database.py'
           '${out_file}'
-          --kraken-db ${kraken_db}
+          --kraken-db ${kraken_db.fields.path}
           --threads \${GALAXY_SLOTS:-1}
           --kmer-len ${kmer_len}
           --read-len ${read_len}
diff -r f25264bb7d6d -r cc49eb0defee data_manager_conf.xml
--- a/data_manager_conf.xml	Wed Jul 31 18:08:06 2019 -0400
+++ b/data_manager_conf.xml	Wed Jul 31 19:09:09 2019 -0400
@@ -4,14 +4,7 @@
             <output>
                 <column name="value"/>
                 <column name="name"/>
-                <column name="path" output_ref="out_file">
-                    <move type="file">
-                        <source>${path}</source>
-                        <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">bracken_databases/${path}</target>
-                   </move>
-                      <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/bracken_databases/${path}</value_translation>
-                      <value_translation type="function">abspath</value_translation>
-                </column>
+                <column name="path" output_ref="out_file"/>
             </output>
         </data_table>
     </data_manager>