# HG changeset patch
# User dfornika
# Date 1556648172 14400
# Node ID bb9833a41c6a4cad07c40cb7eec34a19fc0cb339
# Parent  0aaff8fb824ddb21c6e874f39f8b9bdeb15e6996
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5629d9d7d9836d32b1e501277e213ef213de3e76-dirty

diff -r 0aaff8fb824d -r bb9833a41c6a data_manager/kraken2_build_database.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/kraken2_build_database.py	Tue Apr 30 14:16:12 2019 -0400
@@ -0,0 +1,113 @@
+#!/usr/bin/env python
+
+from __future__ import print_function
+
+import argparse
+import datetime
+import errno
+import json
+import os
+import subprocess
+
+
+DATA_TABLE_NAME = "kraken2_databases"
+
+
+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"]),
+    ])
+
+    database_name = " ".join([
+        "Standard",
+        "(Created:",
+        now + ",",
+        "kmer-len=" + str(kraken2_args["kmer_len"]) + ",",
+        "minimizer-len=" + str(kraken2_args["minimizer_len"]) + ",",
+        "minimizer-spaces=" + str(kraken2_args["minimizer_spaces"]) + ")",
+    ])
+
+    database_path = database_value
+
+    args = [
+        '--threads', str(kraken2_args["threads"]),
+        '--standard',
+        '--kmer-len', str(kraken2_args["kmer_len"]),
+        '--minimizer-len', str(kraken2_args["minimizer_len"]),
+        '--minimizer-spaces', str(kraken2_args["minimizer_spaces"]),
+        '--db', database_path
+    ]
+
+    subprocess.check_call(['kraken2-build'] + args, cwd=target_directory)
+
+    args = [
+        '--threads', str(kraken2_args["threads"]),
+        '--clean',
+        '--db', database_path
+    ]
+
+    subprocess.check_call(['kraken2-build'] + args, cwd=target_directory)
+
+    data_table_entry = {
+        "value": database_value,
+        "name": database_name,
+        "path": database_path,
+    }
+
+    _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, [] )
+    data_manager_dict['data_tables'][data_table_name].append( data_table_entry )
+    return data_manager_dict
+
+
+def main():
+    parser = argparse.ArgumentParser()
+    parser.add_argument('data_manager_json')
+    parser.add_argument( '-k', '--kmer-len', dest='kmer_len', type=int, default=35, help='kmer length' )
+    parser.add_argument( '-m', '--minimizer-len', dest='minimizer_len', type=int, default=31, help='minimizer length' )
+    parser.add_argument( '-s', '--minimizer-spaces', dest='minimizer_spaces', default=6, help='minimizer spaces' )
+    parser.add_argument( '-t', '--threads', dest='threads', default=1, help='threads' )
+    args = parser.parse_args()
+
+    kraken2_args = {
+        "kmer_len": args.kmer_len,
+        "minimizer_len": args.minimizer_len,
+        "minimizer_spaces": args.minimizer_spaces,
+        "threads": args.threads,
+    }
+
+    data_manager_input = json.loads(open(args.data_manager_json).read())
+
+    target_directory = data_manager_input['output_data'][0]['extra_files_path']
+
+    try:
+        os.mkdir( target_directory )
+    except OSError as exc:
+        if exc.errno == errno.EEXIST and os.path.isdir( target_directory ):
+            pass
+        else:
+            raise
+
+    data_manager_output = {}
+
+    kraken2_build_standard(
+        data_manager_output,
+        kraken2_args,
+        target_directory,
+    )
+
+    open(args.data_manager_json, 'w').write(json.dumps(data_manager_output))
+
+
+if __name__ == "__main__":
+    main()
diff -r 0aaff8fb824d -r bb9833a41c6a data_manager/kraken2_build_database.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/kraken2_build_database.xml	Tue Apr 30 14:16:12 2019 -0400
@@ -0,0 +1,51 @@
+<?xml version="1.0"?>
+<tool id="kraken2_build_database" name="Kraken2 Database Builder" tool_type="manage_data" version="2.0.7_beta">
+    <description>database builder</description>
+    <requirements>
+        <requirement type="package" version="2.0.7_beta">kraken2</requirement>
+    </requirements>
+    <version_command>kraken2 -version | head -n 1 | awk '{print $NF}'</version_command>
+    <command detect_errors="exit_code">
+    <![CDATA[
+        python '$__tool_directory__/kraken2_build_database.py'
+          '${out_file}'
+          --threads \${GALAXY_SLOTS:-1}
+          --kmer-len ${kmer_len}
+          --minimizer-len ${minimizer_len}
+          --minimizer-spaces ${minimizer_spaces}
+    ]]>
+    </command>
+    <inputs>
+        <conditional name="database_type">
+            <param name="database_type" type="select" multiple="false" label="Database Type">
+                <option value="standard">Standard</option>
+                <option value="special">Special</option>
+                <option value="custom">Custom</option>
+            </param>
+            <when value="standard">
+            </when>
+            <when value="special">
+                <param name="db_type" type="select" multiple="false" label="Select database to build">
+                    <option value="greengenes">Greengenes</option>
+                    <option value="silva">Silva</option>
+                    <option value="rdp">RDP</option>
+                </param>
+            </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" />
+            </when>
+            <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" />
+        </conditional>
+    </inputs>
+    <outputs>
+        <data name="out_file" format="data_manager_json" />
+    </outputs>
+    <help>
+    </help>
+    <citations>
+        <citation type="doi">10.1186/gb-2014-15-3-r46</citation>
+    </citations>
+</tool>