# HG changeset patch
# User dfornika
# Date 1556926714 14400
# Node ID 2fd3ebc4fcf3f4efa7bacdcba7bc473dd22b753b
# Parent  df30afab73fabae61f88c81e634eb5d329af9948
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 0dd338db82eaa89c790de452b6da4f63e4081b63-dirty

diff -r df30afab73fa -r 2fd3ebc4fcf3 data_manager/kraken2_build_database.py
--- a/data_manager/kraken2_build_database.py	Fri May 03 18:52:15 2019 -0400
+++ b/data_manager/kraken2_build_database.py	Fri May 03 19:38:34 2019 -0400
@@ -195,6 +195,52 @@
     _add_data_table_entry(data_manager_dict, data_table_entry)
 
 
+def kraken2_build_custom(data_manager_dict, kraken2_args, custom_database_name, target_directory, data_table_name=DATA_TABLE_NAME):
+
+    args = [
+        '--threads', str(kraken2_args["threads"]),
+        '--download-taxonomy',
+        '--db', custom_database_name
+    ]
+
+    subprocess.check_call(['kraken2-build'] + args, cwd=target_directory)
+
+    args = [
+        '--threads', str(kraken2_args["threads"]),
+        '--add-to-library', kraken2_args["custom_fasta"],
+        '--db', custom_database_name
+    ]
+
+    subprocess.check_call(['kraken2-build'] + args, cwd=target_directory)
+
+    args = [
+        '--threads', str(kraken2_args["threads"]),
+        '--build',
+        '--kmer-len', str(kraken2_args["kmer_len"]),
+        '--minimizer-len', str(kraken2_args["minimizer_len"]),
+        '--minimizer-spaces', str(kraken2_args["minimizer_spaces"]),
+        '--db', custom_database_name
+    ]
+
+    subprocess.check_call(['kraken2-build'] + args, cwd=target_directory)
+
+    args = [
+        '--threads', str(kraken2_args["threads"]),
+        '--clean',
+        '--db', custom_database_name
+    ]
+
+    subprocess.check_call(['kraken2-build'] + args, target_directory)
+
+    data_table_entry = {
+        "value": custom_database_name,
+        "name": custom_database_name,
+        "path": custom_database_name
+    }
+
+    _add_data_table_entry(data_manager_dict, data_table_name, data_table_entry)
+
+
 def _add_data_table_entry(data_manager_dict, data_table_entry, data_table_name=DATA_TABLE_NAME):
     data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} )
     data_manager_dict['data_tables'][data_table_name] = data_manager_dict['data_tables'].get( data_table_name, [] )
@@ -210,8 +256,10 @@
     parser.add_argument('--minimizer-spaces', dest='minimizer_spaces', default=6, help='minimizer spaces')
     parser.add_argument('--threads', dest='threads', default=1, help='threads')
     parser.add_argument('--database-type', dest='database_type', type=KrakenDatabaseTypes, choices=list(KrakenDatabaseTypes), required=True, help='type of kraken database to build')
-    parser.add_argument( '--minikraken2-version', dest='minikraken2_version', type=Minikraken2Versions, choices=list(Minikraken2Versions), help='MiniKraken2 version' )
+    parser.add_argument('--minikraken2-version', dest='minikraken2_version', type=Minikraken2Versions, choices=list(Minikraken2Versions), help='MiniKraken2 version (only applies to --database-type minikraken)')
     parser.add_argument('--special-database-type', dest='special_database_type', type=SpecialDatabaseTypes, choices=list(SpecialDatabaseTypes), help='type of special database to build (only applies to --database-type special)')
+    parser.add_argument('--custom-fasta', dest='custom_fasta', help='fasta file for custom database (only applies to --database-type custom)')
+    parser.add_argument( '--custom-database-name', dest='custom_database_name', help='Name for custom database (only applies to --database-type custom)' )
     args = parser.parse_args()
 
     data_manager_input = json.loads(open(args.data_manager_json).read())
@@ -260,6 +308,20 @@
             kraken2_args,
             target_directory,
         )
+    elif str(args.database_type) == 'custom':
+        kraken2_args = {
+            "custom_fasta": args.custom_fasta,
+            "kmer_len": args.kmer_len,
+            "minimizer_len": args.minimizer_len,
+            "minimizer_spaces": args.minimizer_spaces,
+            "threads": args.threads,
+        }
+        kraken2_build_custom(
+            data_manager_output,
+            kraken2_args,
+            args.custom_database_name,
+            target_directory,
+        )
     else:
         sys.exit("Invalid database type")
 
diff -r df30afab73fa -r 2fd3ebc4fcf3 data_manager/kraken2_build_database.xml
--- a/data_manager/kraken2_build_database.xml	Fri May 03 18:52:15 2019 -0400
+++ b/data_manager/kraken2_build_database.xml	Fri May 03 19:38:34 2019 -0400
@@ -30,6 +30,13 @@
             --kmer-len ${database_type.kmer_len}
             --minimizer-len ${database_type.minimizer_len}
             --minimizer-spaces ${database_type.minimizer_spaces}
+          #else if $database_type.database_type == "custom"
+            --threads \${GALAXY_SLOTS:-1}
+            --custom-fasta ${database_type.custom_fasta}
+            --custom-database-name ${database_type.custom_database_name}
+            --kmer-len ${database_type.kmer_len}
+            --minimizer-len ${database_type.minimizer_len}
+            --minimizer-spaces ${database_type.minimizer_spaces}
           #end if
     ]]>
     </command>
@@ -59,8 +66,8 @@
                 <expand macro="common_params" />
             </when>
             <when value="custom">
-                <param name="input_fasta" type="data" format="fasta" multiple="False" optional="true" label="Select history item" />
-                <param name="database_name" type="text" label="Name for this database" />
+                <param name="custom_fasta" type="data" format="fasta" multiple="False" optional="true" label="Select history item" />
+                <param name="custom_database_name" type="text" label="Name for this database" />
                 <expand macro="common_params" />
             </when>