# HG changeset patch
# User dfornika
# Date 1635978868 0
# Node ID 80e778af6c6c7dc3186b21384a84152ccd0111bb
# Parent  38c99b2942645ad6951b38f2463a747c05e6fd81
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 57b36cfbdd1663aef43d03b76e37364cc5bdeef3-dirty"

diff -r 38c99b294264 -r 80e778af6c6c data_manager/kraken2_build_database.py
--- a/data_manager/kraken2_build_database.py	Wed Oct 23 14:18:06 2019 -0400
+++ b/data_manager/kraken2_build_database.py	Wed Nov 03 22:34:28 2021 +0000
@@ -59,6 +59,7 @@
         "kmer-len", str(kraken2_args["kmer_len"]),
         "minimizer-len", str(kraken2_args["minimizer_len"]),
         "minimizer-spaces", str(kraken2_args["minimizer_spaces"]),
+        "load-factor", str(kraken2_args["load_factor"]),
     ])
 
     database_name = " ".join([
@@ -68,6 +69,7 @@
         "kmer-len=" + str(kraken2_args["kmer_len"]) + ",",
         "minimizer-len=" + str(kraken2_args["minimizer_len"]) + ",",
         "minimizer-spaces=" + str(kraken2_args["minimizer_spaces"]) + ")",
+        "load-factor", str(kraken2_args["load_factor"]),
     ])
 
     database_path = database_value
@@ -78,6 +80,7 @@
         '--kmer-len', str(kraken2_args["kmer_len"]),
         '--minimizer-len', str(kraken2_args["minimizer_len"]),
         '--minimizer-spaces', str(kraken2_args["minimizer_spaces"]),
+        '--load-factor', str(kraken2_args["load_factor"]),
         '--db', database_path
     ]
 
@@ -129,7 +132,7 @@
 
     # download the minikraken2 data
     src = urlopen(
-        'ftp://ftp.ccb.jhu.edu/pub/data/kraken2_dbs/minikraken2_%s_8GB_201904_UPDATE.tgz'
+        'https://genome-idx.s3.amazonaws.com/kraken/minikraken2_%s_8GB_201904.tgz'
         % minikraken2_version
     )
     with open('tmp_data.tar.gz', 'wb') as dst:
@@ -172,6 +175,7 @@
         "kmer-len", str(kraken2_args["kmer_len"]),
         "minimizer-len", str(kraken2_args["minimizer_len"]),
         "minimizer-spaces", str(kraken2_args["minimizer_spaces"]),
+        "load-factor", str(kraken2_args["load_factor"]),
     ])
 
     database_name = " ".join([
@@ -181,6 +185,7 @@
         "kmer-len=" + str(kraken2_args["kmer_len"]) + ",",
         "minimizer-len=" + str(kraken2_args["minimizer_len"]) + ",",
         "minimizer-spaces=" + str(kraken2_args["minimizer_spaces"]) + ")",
+        "load-factor=" + str(kraken2_args["load_factor"]) + ")",
     ])
 
     database_path = database_value
@@ -191,6 +196,7 @@
         '--kmer-len', str(kraken2_args["kmer_len"]),
         '--minimizer-len', str(kraken2_args["minimizer_len"]),
         '--minimizer-spaces', str(kraken2_args["minimizer_spaces"]),
+        '--load-factor', str(kraken2_args["load_factor"]),
         '--db', database_path
     ]
 
@@ -247,6 +253,7 @@
         '--kmer-len', str(kraken2_args["kmer_len"]),
         '--minimizer-len', str(kraken2_args["minimizer_len"]),
         '--minimizer-spaces', str(kraken2_args["minimizer_spaces"]),
+        '--load-factor', str(kraken2_args["load_factor"]),
         '--db', custom_database_name
     ]
 
@@ -282,6 +289,7 @@
     parser.add_argument('--kmer-len', dest='kmer_len', type=int, default=35, help='kmer length')
     parser.add_argument('--minimizer-len', dest='minimizer_len', type=int, default=31, help='minimizer length')
     parser.add_argument('--minimizer-spaces', dest='minimizer_spaces', default=6, help='minimizer spaces')
+    parser.add_argument('--load-factor', dest='load_factor', type=float, default=0.7, help='load factor')
     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 (only applies to --database-type minikraken)')
@@ -292,14 +300,15 @@
     parser.add_argument('--clean', dest='clean', action='store_true', help='Clean up extra files')
     args = parser.parse_args()
 
-    data_manager_input = json.loads(open(args.data_manager_json).read())
+    with open(args.data_manager_json) as fh:
+        data_manager_input = json.load(fh)
 
     target_directory = data_manager_input['output_data'][0]['extra_files_path']
 
     try:
-        os.mkdir( target_directory )
+        os.mkdir(target_directory)
     except OSError as exc:
-        if exc.errno == errno.EEXIST and os.path.isdir( target_directory ):
+        if exc.errno == errno.EEXIST and os.path.isdir(target_directory):
             pass
         else:
             raise
@@ -311,6 +320,7 @@
             "kmer_len": args.kmer_len,
             "minimizer_len": args.minimizer_len,
             "minimizer_spaces": args.minimizer_spaces,
+            "load_factor": args.load_factor,
             "threads": args.threads,
             "clean": args.clean,
         }
@@ -329,6 +339,7 @@
             "kmer_len": args.kmer_len,
             "minimizer_len": args.minimizer_len,
             "minimizer_spaces": args.minimizer_spaces,
+            "load_factor": args.load_factor,
             "threads": args.threads,
             "clean": args.clean,
         }
@@ -343,6 +354,7 @@
             "kmer_len": args.kmer_len,
             "minimizer_len": args.minimizer_len,
             "minimizer_spaces": args.minimizer_spaces,
+            "load_factor": args.load_factor,
             "threads": args.threads,
             "clean": args.clean,
         }
@@ -354,7 +366,8 @@
     else:
         sys.exit("Invalid database type")
 
-    open(args.data_manager_json, 'w').write(json.dumps(data_manager_output))
+    with open(args.data_manager_json, 'w') as fh:
+        json.dump(data_manager_output, fh, sort_keys=True)
 
 
 if __name__ == "__main__":
diff -r 38c99b294264 -r 80e778af6c6c data_manager/kraken2_build_database.xml
--- a/data_manager/kraken2_build_database.xml	Wed Oct 23 14:18:06 2019 -0400
+++ b/data_manager/kraken2_build_database.xml	Wed Nov 03 22:34:28 2021 +0000
@@ -1,16 +1,19 @@
 <?xml version="1.0"?>
-<tool id="kraken2_build_database" name="Kraken2" tool_type="manage_data" version="2.0.8_beta_galaxy1">
+<tool id="kraken2_build_database" name="Kraken2" tool_type="manage_data" version="@TOOL_VERSION@" profile="18.09">
     <macros>
+        <token name="@TOOL_VERSION@">2.1.1</token>
         <xml name="common_params">
             <param name="kmer_len" type="integer" value="35" label="K-mer length in BP" />
             <param name="minimizer_len" type="integer" value="31" label="Minimizer length" />
             <param name="minimizer_spaces" type="integer" value="6" label="Minimizer spaces" />
+            <param name="load_factor" type="float" value="0.7" min="0" max="1" label="Load factor" help="Proportion of the hash table to be populated" />
             <param name="clean" type="boolean" truevalue="--clean" falsevalue="" checked="true" label="Clean up extra files" />
         </xml>
     </macros>
     <description>database builder</description>
     <requirements>
-        <requirement type="package" version="2.0.8_beta">kraken2</requirement>
+        <requirement type="package" version="@TOOL_VERSION@">kraken2</requirement>
+        <requirement type="package" version="3.7">python</requirement>
     </requirements>
     <version_command>kraken2 -version | head -n 1 | awk '{print $NF}'</version_command>
     <command detect_errors="exit_code">
@@ -25,6 +28,7 @@
             --kmer-len ${database_type.kmer_len}
             --minimizer-len ${database_type.minimizer_len}
             --minimizer-spaces ${database_type.minimizer_spaces}
+            --load-factor ${database_type.load_factor}
             ${database_type.clean}
           #else if $database_type.database_type == "special"
             --threads \${GALAXY_SLOTS:-1}
@@ -32,6 +36,7 @@
             --kmer-len ${database_type.kmer_len}
             --minimizer-len ${database_type.minimizer_len}
             --minimizer-spaces ${database_type.minimizer_spaces}
+            --load-factor ${database_type.load_factor}
             ${database_type.clean}
           #else if $database_type.database_type == "custom"
             --threads \${GALAXY_SLOTS:-1}
@@ -41,6 +46,7 @@
             --kmer-len ${database_type.kmer_len}
             --minimizer-len ${database_type.minimizer_len}
             --minimizer-spaces ${database_type.minimizer_spaces}
+            --load-factor ${database_type.load_factor}
             ${database_type.clean}
           #end if
     ]]>
diff -r 38c99b294264 -r 80e778af6c6c data_manager_conf.xml
--- a/data_manager_conf.xml	Wed Oct 23 14:18:06 2019 -0400
+++ b/data_manager_conf.xml	Wed Nov 03 22:34:28 2021 +0000
@@ -1,5 +1,5 @@
 <data_managers>
-    <data_manager tool_file="data_manager/kraken2_build_database.xml" id="kraken2_build_database" version="2.0.8_beta_galaxy1">
+    <data_manager tool_file="data_manager/kraken2_build_database.xml" id="kraken2_build_database" version="2.0.8_beta+galaxy1">
         <data_table name="kraken2_databases">
             <output>
                 <column name="value"/>
diff -r 38c99b294264 -r 80e778af6c6c test-data/kraken2_custom_data_manager.json
--- a/test-data/kraken2_custom_data_manager.json	Wed Oct 23 14:18:06 2019 -0400
+++ b/test-data/kraken2_custom_data_manager.json	Wed Nov 03 22:34:28 2021 +0000
@@ -1,1 +1,1 @@
-{"data_tables": {"kraken2_databases": [{"path": "database", "name": "database", "value": "database"}]}}
\ No newline at end of file
+{"data_tables": {"kraken2_databases": [{"name": "database", "path": "database", "value": "database"}]}}
\ No newline at end of file