changeset 52:86bc169b0aeb draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 1137710d16538da15bcd87e1ba382e2afc00031f-dirty

--- a/data_manager/kraken2_build_custom.py	Fri May 03 19:38:34 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,113 +0,0 @@
-#!/usr/bin/env python
-
-from __future__ import print_function
-
-import argparse
-import errno
-import json
-import os
-import subprocess
-
-
-DATA_TABLE_NAME = "kraken2_databases"
-
-
-def kraken2_build(data_manager_dict, kraken2_args, database_name, target_directory, data_table_name=DATA_TABLE_NAME):
-
-    args = [
-        '--threads', str(kraken2_args["threads"]),
-        '--download-taxonomy',
-        '--db', database_name
-    ]
-
-    subprocess.check_call(['kraken2-build'] + args, cwd=target_directory)
-
-    args = [
-        '--threads', str(kraken2_args["threads"]),
-        '--add-to-library', kraken2_args["fasta"],
-        '--db', 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', database_name
-    ]
-
-    subprocess.check_call(['kraken2-build'] + args, cwd=target_directory)
-
-    args = [
-        '--threads', str(kraken2_args["threads"]),
-        '--clean',
-        '--db', database_name
-    ]
-
-    subprocess.check_call(['kraken2-build'] + args, target_directory)
-
-    data_table_entry = {
-        "value": database_name,
-        "name": database_name,
-        "path": 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_name, data_table_entry):
-    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('params')
-    parser.add_argument( '-d', '--db', dest='database_name', help='database name' )
-    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( '-f', '--fasta', dest='fasta', help='fasta' )
-    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,
-        "fasta": args.fasta,
-        "threads": args.threads,
-    }
-
-    params = json.loads(open(args.params).read())
-    target_directory = params['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_dict = {}
-
-    # build the index
-    kraken2_build(
-        data_manager_dict,
-        kraken2_args,
-        args.database_name,
-        target_directory
-    )
-
-    # save info to json file
-    open(args.params, 'w').write(json.dumps(data_manager_dict))
-
-
-if __name__ == "__main__":
-    main()

--- a/data_manager/kraken2_build_custom.xml	Fri May 03 19:38:34 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,35 +0,0 @@
-<?xml version="1.0"?>
-<tool id="kraken2_build_custom" name="Kraken2 Custom Database Builder" tool_type="manage_data" version="2.0.8_beta">
-    <description>database builder</description>
-    <requirements>
-        <requirement type="package" version="2.0.8_beta">kraken2</requirement>
-    </requirements>
-    <version_command>kraken2 -version | head -n 1 | awk '{print $NF}'</version_command>
-    <command detect_errors="exit_code">
-    <![CDATA[
-        python '$__tool_directory__/kraken2_build_custom.py'
-          '${out_file}'
-          --threads \${GALAXY_SLOTS:-1}
-          --db '${database_name}'
-          --kmer-len ${kmer_len}
-          --minimizer-len ${minimizer_len}
-          --minimizer-spaces ${minimizer_spaces}
-          --fasta ${input_fasta}
-    ]]>
-    </command>
-    <inputs>
-        <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="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" />
-    </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>

--- a/data_manager/kraken2_build_database.py	Fri May 03 19:38:34 2019 -0400
+++ b/data_manager/kraken2_build_database.py	Wed May 08 18:39:03 2019 -0400
@@ -50,7 +50,7 @@
         return self.value
 
 
-def kraken2_build_standard(data_manager_dict, kraken2_args, target_directory, data_table_name=DATA_TABLE_NAME):
+def kraken2_build_standard(kraken2_args, target_directory, data_table_name=DATA_TABLE_NAME):
     now = datetime.datetime.utcnow().strftime("%Y-%m-%dT%H%M%SZ")
 
     database_value = "_".join([
@@ -92,15 +92,21 @@
     subprocess.check_call(['kraken2-build'] + args, cwd=target_directory)
 
     data_table_entry = {
-        "value": database_value,
-        "name": database_name,
-        "path": database_path,
+        'data_tables': {
+            data_table_name: [
+                {
+                    "value": database_value,
+                    "name": database_name,
+                    "path": database_path,
+                }
+            ]
+        }
     }
 
-    _add_data_table_entry(data_manager_dict, data_table_entry)
+    return data_table_entry
 
 
-def kraken2_build_minikraken(data_manager_dict, minikraken2_version, target_directory, data_table_name=DATA_TABLE_NAME):
+def kraken2_build_minikraken(minikraken2_version, target_directory, data_table_name=DATA_TABLE_NAME):
 
     now = datetime.datetime.utcnow().strftime("%Y-%m-%dT%H%M%SZ")
 
@@ -130,15 +136,21 @@
         fh.extractall(target_directory)
 
     data_table_entry = {
-        "value": database_value,
-        "name": database_name,
-        "path": database_value,
+        'data_tables': {
+            data_table_name: [
+                {
+                    "value": database_value,
+                    "name": database_name,
+                    "path": database_value,
+                }
+            ]
+        }
     }
 
-    _add_data_table_entry(data_manager_dict, data_table_entry)
+    return data_table_entry
 
 
-def kraken2_build_special(data_manager_dict, kraken2_args, target_directory, data_table_name=DATA_TABLE_NAME):
+def kraken2_build_special(kraken2_args, target_directory, data_table_name=DATA_TABLE_NAME):
 
     now = datetime.datetime.utcnow().strftime("%Y-%m-%dT%H%M%SZ")
 
@@ -187,15 +199,21 @@
     subprocess.check_call(['kraken2-build'] + args, cwd=target_directory)
 
     data_table_entry = {
-        "value": database_value,
-        "name": database_name,
-        "path": database_path,
+        'data_tables': {
+            data_table_name: [
+                {
+                    "value": database_value,
+                    "name": database_name,
+                    "path": database_path,
+                }
+            ]
+        }
     }
 
-    _add_data_table_entry(data_manager_dict, data_table_entry)
+    return data_table_entry
 
 
-def kraken2_build_custom(data_manager_dict, kraken2_args, custom_database_name, target_directory, data_table_name=DATA_TABLE_NAME):
+def kraken2_build_custom(kraken2_args, custom_database_name, target_directory, data_table_name=DATA_TABLE_NAME):
 
     args = [
         '--threads', str(kraken2_args["threads"]),
@@ -233,24 +251,23 @@
     subprocess.check_call(['kraken2-build'] + args, target_directory)
 
     data_table_entry = {
-        "value": custom_database_name,
-        "name": custom_database_name,
-        "path": custom_database_name
+        'data_tables': {
+            data_table_name: [
+                {
+                    "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, [] )
-    data_manager_dict['data_tables'][data_table_name].append( data_table_entry )
-    return data_manager_dict
+    return data_table_entry
 
 
 def main():
     parser = argparse.ArgumentParser()
-    parser.add_argument('data_manager_json')
+    parser.add_argument('--extra-files-path', dest='extra_files_path', help='')
     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')
@@ -259,12 +276,12 @@
     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)' )
+    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())
 
-    target_directory = data_manager_input['output_data'][0]['extra_files_path']
+    target_directory = args.extra_files_path
 
     try:
         os.mkdir( target_directory )
@@ -276,7 +293,6 @@
 
     data_manager_output = {}
 
-    print(args.database_type)
     if str(args.database_type) == 'standard':
         kraken2_args = {
             "kmer_len": args.kmer_len,
@@ -284,14 +300,12 @@
             "minimizer_spaces": args.minimizer_spaces,
             "threads": args.threads,
         }
-        kraken2_build_standard(
-            data_manager_output,
+        data_manager_output = kraken2_build_standard(
             kraken2_args,
             target_directory,
         )
     elif str(args.database_type) == 'minikraken':
-        kraken2_build_minikraken(
-            data_manager_output,
+        data_manager_output = kraken2_build_minikraken(
             str(args.minikraken2_version),
             target_directory
         )
@@ -303,8 +317,7 @@
             "minimizer_spaces": args.minimizer_spaces,
             "threads": args.threads,
         }
-        kraken2_build_special(
-            data_manager_output,
+        data_manager_output = kraken2_build_special(
             kraken2_args,
             target_directory,
         )
@@ -316,8 +329,7 @@
             "minimizer_spaces": args.minimizer_spaces,
             "threads": args.threads,
         }
-        kraken2_build_custom(
-            data_manager_output,
+        data_manager_output = kraken2_build_custom(
             kraken2_args,
             args.custom_database_name,
             target_directory,

--- a/data_manager/kraken2_build_database.xml	Fri May 03 19:38:34 2019 -0400
+++ b/data_manager/kraken2_build_database.xml	Wed May 08 18:39:03 2019 -0400
@@ -15,7 +15,7 @@
     <command detect_errors="exit_code">
     <![CDATA[
         python '$__tool_directory__/kraken2_build_database.py'
-          '${out_file}'
+          --extra-files-path '$out_file.extra_files_path'
           --database-type ${database_type.database_type}
           #if $database_type.database_type == "minikraken"
             --minikraken2-version ${database_type.minikraken2_version}

--- a/data_manager/kraken2_build_minikraken.py	Fri May 03 19:38:34 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,100 +0,0 @@
-#!/usr/bin/env python
-
-from __future__ import print_function
-
-import argparse
-import datetime
-import errno
-import json
-import os
-import shutil
-import tarfile
-
-try:
-    # Python3
-    from urllib.request import urlopen
-except ImportError:
-    from urllib2 import urlopen
-
-
-DATA_TABLE_NAME = "kraken2_databases"
-
-
-def kraken2_build_minikraken(data_manager_dict, minikraken2_version, target_directory, data_table_name=DATA_TABLE_NAME):
-
-    now = datetime.datetime.utcnow().strftime("%Y-%m-%dT%H%M%SZ")
-
-    database_value = "_".join([
-        now,
-        "minikraken2",
-        minikraken2_version,
-        "8GB",
-    ])
-
-    database_name = " ".join([
-        "Minikraken2",
-        minikraken2_version,
-        "(Created:",
-        now + ")"
-    ])
-
-    # download the minikraken2 data
-    src = urlopen(
-        'ftp://ftp.ccb.jhu.edu/pub/data/kraken2_dbs/minikraken2_%s_8GB_201904_UPDATE.tgz'
-        % minikraken2_version
-    )
-    with open('tmp_data.tar.gz', 'wb') as dst:
-        shutil.copyfileobj(src, dst)
-    # unpack the downloaded archive to the target directory
-    with tarfile.open('tmp_data.tar.gz', 'r:gz') as fh:
-        fh.extractall(target_directory)
-
-    data_table_entry = {
-        "value": database_value,
-        "name": database_name,
-        "path": database_value,
-    }
-
-    _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( '-v', '--minikraken2-version', dest='minikraken2_version', default="v2", help='MiniKraken2 version (v1 or v2)' )
-    parser.add_argument( '-t', '--threads', dest='threads', default=1, help='threads' )
-
-    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']
-
-    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_minikraken(
-        data_manager_output,
-        args.minikraken2_version,
-        target_directory,
-    )
-
-    open(args.data_manager_json, 'w').write(json.dumps(data_manager_output))
-
-
-if __name__ == "__main__":
-    main()

--- a/data_manager/kraken2_build_minikraken.xml	Fri May 03 19:38:34 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,30 +0,0 @@
-<?xml version="1.0"?>
-<tool id="kraken2_build_minikraken" name="Kraken2 MiniKraken2 Database Builder" tool_type="manage_data" version="2.0.8_beta">
-    <description>database builder</description>
-    <requirements>
-        <requirement type="package" version="2.0.8_beta">kraken2</requirement>
-    </requirements>
-    <version_command>kraken2 -version | head -n 1 | awk '{print $NF}'</version_command>
-    <command detect_errors="exit_code">
-    <![CDATA[
-        python '$__tool_directory__/kraken2_build_minikraken.py'
-          '${out_file}'
-          --threads \${GALAXY_SLOTS:-1}
-	  --minikraken2-version ${minikraken2_version}
-    ]]>
-    </command>
-    <inputs>
-      <param name="minikraken2_version" type="select" multiple="false" label="Select MiniKraken2 database version to download">
-	    <option value="v2">Version 2</option>
-            <option value="v1">Version 1</option>
-        </param>
-    </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>

--- a/data_manager/kraken2_build_special.py	Fri May 03 19:38:34 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,122 +0,0 @@
-#!/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")
-
-    special_database_names = {
-        "rdp": "RDP",
-        "greengenes": "Greengenes",
-        "silva": "Silva",
-    }
-
-    database_value = "_".join([
-        now,
-        kraken2_args["special"],
-        "kmer-len", str(kraken2_args["kmer_len"]),
-        "minimizer-len", str(kraken2_args["minimizer_len"]),
-        "minimizer-spaces", str(kraken2_args["minimizer_spaces"]),
-    ])
-
-    database_name = " ".join([
-        special_database_names[kraken2_args["special"]],
-        "(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"]),
-        '--special', kraken2_args["special"],
-        '--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( '-b', '--db-type', dest='db_type', help='database type (one of: silva, rdp, greengenes)' )
-    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 = {
-        "special": args.db_type,
-        "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()

--- a/data_manager/kraken2_build_special.xml	Fri May 03 19:38:34 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,37 +0,0 @@
-<?xml version="1.0"?>
-<tool id="kraken2_build_special" name="Kraken2 Special Database Builder" tool_type="manage_data" version="2.0.8_beta">
-    <description>database builder</description>
-    <requirements>
-        <requirement type="package" version="2.0.8_beta">kraken2</requirement>
-    </requirements>
-    <version_command>kraken2 -version | head -n 1 | awk '{print $NF}'</version_command>
-    <command detect_errors="exit_code">
-    <![CDATA[
-        python '$__tool_directory__/kraken2_build_special.py'
-          '${out_file}'
-	  --db-type ${db_type}
-          --threads \${GALAXY_SLOTS:-1}
-          --kmer-len ${kmer_len}
-          --minimizer-len ${minimizer_len}
-          --minimizer-spaces ${minimizer_spaces}
-    ]]>
-    </command>
-    <inputs>
-        <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>
-        <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" />
-    </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>

--- a/data_manager/kraken2_build_standard.py	Fri May 03 19:38:34 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,113 +0,0 @@
-#!/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()

--- a/data_manager/kraken2_build_standard.xml	Fri May 03 19:38:34 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,31 +0,0 @@
-<?xml version="1.0"?>
-<tool id="kraken2_build_standard" name="Kraken2 Standard Database Builder" tool_type="manage_data" version="2.0.8_beta">
-    <description>database builder</description>
-    <requirements>
-        <requirement type="package" version="2.0.8_beta">kraken2</requirement>
-    </requirements>
-    <version_command>kraken2 -version | head -n 1 | awk '{print $NF}'</version_command>
-    <command detect_errors="exit_code">
-    <![CDATA[
-        python '$__tool_directory__/kraken2_build_standard.py'
-          '${out_file}'
-          --threads \${GALAXY_SLOTS:-1}
-          --kmer-len ${kmer_len}
-          --minimizer-len ${minimizer_len}
-          --minimizer-spaces ${minimizer_spaces}
-    ]]>
-    </command>
-    <inputs>
-        <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" />
-    </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>

--- a/data_manager_conf.xml	Fri May 03 19:38:34 2019 -0400
+++ b/data_manager_conf.xml	Wed May 08 18:39:03 2019 -0400
@@ -1,18 +1,18 @@
 <data_managers>
     <data_manager tool_file="data_manager/kraken2_build_database.xml" id="kraken2_build_database" version="1.0">
-	<data_table name="kraken2_databases">
-	    <output>
-		<column name="value"/>
-		<column name="name"/>
-		<column name="path" output_ref="out_file">
-		    <move type="directory">
-		        <source>${path}</source>
-			<target base="${GALAXY_DATA_MANAGER_DATA_PATH}">kraken2_databases/${path}</target>
-		    </move>
+        <data_table name="kraken2_databases">
+            <output>
+                <column name="value"/>
+                <column name="name"/>
+                <column name="path" output_ref="out_file">
+                    <move type="directory">
+                        <source>${path}</source>
+                        <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">kraken2_databases/${path}</target>
+                    </move>
                     <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/kraken2_databases/${path}</value_translation>
-		    <value_translation type="function">abspath</value_translation>
-		</column>
-	    </output>
-	</data_table>
+                    <value_translation type="function">abspath</value_translation>
+                </column>
+            </output>
+        </data_table>
     </data_manager>
 </data_managers>