changeset 45:86a86acfa13c draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit a7d56007dd2065b053a3102b5f0e693aa5ddaedf-dirty

--- a/data_manager/kraken2_build_database.py	Thu May 02 19:27:42 2019 -0400
+++ b/data_manager/kraken2_build_database.py	Fri May 03 17:27:29 2019 -0400
@@ -10,7 +10,7 @@
 import shutil
 import subprocess
 import sys
-
+import tarfile
 from enum import Enum
 
 try:
@@ -22,6 +22,7 @@
 
 DATA_TABLE_NAME = "kraken2_databases"
 
+
 class KrakenDatabaseTypes(Enum):
     standard = 'standard'
     minikraken = 'minikraken'
@@ -31,6 +32,7 @@
     def __str__(self):
         return self.value
 
+
 class Minikraken2Versions(Enum):
     v1 = 'v1'
     v2 = 'v2'
@@ -38,15 +40,16 @@
     def __str__(self):
         return self.value
 
+
 def kraken2_build_standard(data_manager_dict, kraken2_args, target_directory, data_table_name=DATA_TABLE_NAME):
     now = datetime.datetime.utcnow().strftime("%Y-%m-%dT%H%M%SZ")
 
     database_value = "_".join([
         now,
         "standard",
-        "kmer-len" + str(kraken2_args["kmer_len"]),
-        "minimizer-len" + str(kraken2_args["minimizer_len"]),
-        "minimizer-spaces" + str(kraken2_args["minimizer_spaces"]),
+        "kmer-len", str(kraken2_args["kmer_len"]),
+        "minimizer-len", str(kraken2_args["minimizer_len"]),
+        "minimizer-spaces", str(kraken2_args["minimizer_spaces"]),
     ])
 
     database_name = " ".join([
@@ -125,6 +128,7 @@
 
     _add_data_table_entry(data_manager_dict, 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, [] )
@@ -143,7 +147,6 @@
     parser.add_argument( '--minikraken2-version', dest='minikraken2_version', type=Minikraken2Versions, choices=list(Minikraken2Versions), help='MiniKraken2 version' )
     args = parser.parse_args()
 
-
     data_manager_input = json.loads(open(args.data_manager_json).read())
 
     target_directory = data_manager_input['output_data'][0]['extra_files_path']

--- a/data_manager/kraken2_build_database.xml	Thu May 02 19:27:42 2019 -0400
+++ b/data_manager/kraken2_build_database.xml	Fri May 03 17:27:29 2019 -0400
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool id="kraken2_build_database" name="Kraken2 Database Builder" tool_type="manage_data" version="2.0.7_beta">
+<tool id="kraken2_build_database" name="Kraken2 Database Builder" tool_type="manage_data" version="2.0.8_beta">
     <macros>
         <xml name="common_params">
             <param name="kmer_len" type="integer" value="35" label="K-mer length in BP" />
@@ -9,7 +9,7 @@
     </macros>
     <description>database builder</description>
     <requirements>
-        <requirement type="package" version="2.0.7_beta">kraken2</requirement>
+        <requirement type="package" version="2.0.8_beta">kraken2</requirement>
     </requirements>
     <version_command>kraken2 -version | head -n 1 | awk '{print $NF}'</version_command>
     <command detect_errors="exit_code">