# HG changeset patch
# User dfornika
# Date 1513809363 18000
# Node ID 1d9e3950ce61a0adc231f6046d97a52cde004edb
planemo upload for repository https://github.com/WGS-TB/MentaLiST/tree/master/galaxy commit 77d12d12820477cdb046be90175f5d2dab52e620
diff -r 000000000000 -r 1d9e3950ce61 data_managers/data_manager_conf.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_managers/data_manager_conf.xml Wed Dec 20 17:36:03 2017 -0500
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diff -r 000000000000 -r 1d9e3950ce61 data_managers/data_manager_mentalist_build_db/data_manager/mentalist_build_db.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_managers/data_manager_mentalist_build_db/data_manager/mentalist_build_db.py Wed Dec 20 17:36:03 2017 -0500
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+#!/usr/bin/env python
+from __future__ import print_function
+
+import argparse
+import os
+import subprocess
+import sys
+import errno
+from json import dumps, loads
+
+DEFAULT_DATA_TABLE_NAMES = ["mentalist_databases"]
+
+
+def mentalist_build_db( data_manager_dict, database_name, kmer_size, profile, fasta_files, params, target_directory, data_table_names=DEFAULT_DATA_TABLE_NAMES ):
+ args = [ 'mentalist', 'build_db', '--db', database_name, '-k', str(kmer_size)]
+ if profile:
+ args += ['--profile', profile]
+ print(args)
+ args += ['--fasta_files'] + fasta_files
+ proc = subprocess.Popen( args=args, shell=False, cwd=target_directory )
+ return_code = proc.wait()
+ if return_code:
+ print("Error building database.", file=sys.stderr)
+ sys.exit( return_code )
+ data_table_entry = dict( value=database_name, dbkey=database_name, name=database_name, path=database_name )
+ for data_table_name in data_table_names:
+ _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', default=None, help='Database Name' )
+ parser.add_argument( '-f', '--fasta_files', dest='fasta_files', nargs='+', default=None, help='FASTA Filenames' )
+ parser.add_argument( '-k', '--kmer_size', dest='kmer_size', type=int, default=None, help='kmer Size' )
+ parser.add_argument( '-p', '--profile', dest='profile', type=int, default=None, help='Profile' )
+ args = parser.parse_args()
+
+ params = 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
+ mentalist_build_db( data_manager_dict, args.database_name, args.kmer_size, args.profile, args.fasta_files, params, target_directory, DEFAULT_DATA_TABLE_NAMES )
+
+ # save info to json file
+ open( args.params, 'wb' ).write( dumps( data_manager_dict ) )
+
+
+if __name__ == "__main__":
+ main()
diff -r 000000000000 -r 1d9e3950ce61 data_managers/data_manager_mentalist_build_db/data_manager/mentalist_build_db.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_managers/data_manager_mentalist_build_db/data_manager/mentalist_build_db.xml Wed Dec 20 17:36:03 2017 -0500
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+ mentalist
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+ 10.1101/172858
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diff -r 000000000000 -r 1d9e3950ce61 data_managers/data_manager_mentalist_build_db/tool-data/mentalist_databases.loc.sample
diff -r 000000000000 -r 1d9e3950ce61 data_managers/data_manager_mentalist_build_db/tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_managers/data_manager_mentalist_build_db/tool_data_table_conf.xml.sample Wed Dec 20 17:36:03 2017 -0500
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diff -r 000000000000 -r 1d9e3950ce61 data_managers/data_manager_mentalist_download_cgmlst/data_manager/mentalist_download_cgmlst.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_managers/data_manager_mentalist_download_cgmlst/data_manager/mentalist_download_cgmlst.py Wed Dec 20 17:36:03 2017 -0500
@@ -0,0 +1,73 @@
+#!/usr/bin/env python
+
+from __future__ import print_function
+
+import argparse
+import datetime
+import errno
+import os
+import string
+import subprocess
+import sys
+
+from json import dumps, loads
+
+
+DEFAULT_DATA_TABLE_NAMES = ["mentalist_databases"]
+
+
+def mentalist_download_cgmlst( data_manager_dict, kmer_size, scheme, params, target_directory, data_table_names=DEFAULT_DATA_TABLE_NAMES ):
+ translation_table = string.maketrans(string.punctuation, ("_" * 32))
+ base_path = scheme.lower().replace(" ", "_").translate(translation_table) + "_cgmlst"
+ today = datetime.date.today().isoformat()
+ scheme_files_path = base_path + "_scheme_" + today
+ database_path = base_path + "_k" + str(kmer_size) + "_" + today
+ database_name = base_path + "_k" + str(kmer_size) + "_" + today + ".jld"
+ display_name = scheme + " k=" + str(kmer_size) + " (cgMLST) " + today
+ args = [ 'mentalist', 'download_cgmlst', '-s', scheme, '-k', str(kmer_size), '--db', database_name, '-o', scheme_files_path]
+ proc = subprocess.Popen( args=args, shell=False, cwd=target_directory )
+ return_code = proc.wait()
+ if return_code:
+ print("Error building database.", file=sys.stderr)
+ sys.exit( return_code )
+ data_table_entry = dict( value=database_path, dbkey='cgMLST', name=display_name, path=database_name )
+ for data_table_name in data_table_names:
+ _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( '-k', '--kmer_size', dest='kmer_size', type=int, default=None, help='kmer Size' )
+ parser.add_argument( '-s', '--scheme', dest='scheme', default=None, help='Scheme' )
+ args = parser.parse_args()
+
+ params = 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
+ mentalist_download_cgmlst( data_manager_dict, args.kmer_size, args.scheme, params, target_directory, DEFAULT_DATA_TABLE_NAMES )
+
+ # save info to json file
+ open( args.params, 'wb' ).write( dumps( data_manager_dict ) )
+
+
+if __name__ == "__main__":
+ main()
diff -r 000000000000 -r 1d9e3950ce61 data_managers/data_manager_mentalist_download_cgmlst/data_manager/mentalist_download_cgmlst.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_managers/data_manager_mentalist_download_cgmlst/data_manager/mentalist_download_cgmlst.xml Wed Dec 20 17:36:03 2017 -0500
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diff -r 000000000000 -r 1d9e3950ce61 data_managers/data_manager_mentalist_download_cgmlst/tool-data/mentalist_databases.loc.sample
diff -r 000000000000 -r 1d9e3950ce61 data_managers/data_manager_mentalist_download_cgmlst/tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_managers/data_manager_mentalist_download_cgmlst/tool_data_table_conf.xml.sample Wed Dec 20 17:36:03 2017 -0500
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diff -r 000000000000 -r 1d9e3950ce61 data_managers/data_manager_mentalist_download_pubmlst/data_manager/mentalist_download_pubmlst.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_managers/data_manager_mentalist_download_pubmlst/data_manager/mentalist_download_pubmlst.py Wed Dec 20 17:36:03 2017 -0500
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+#!/usr/bin/env python
+
+from __future__ import print_function
+
+import argparse
+import datetime
+import errno
+import os
+import string
+import subprocess
+import sys
+
+from json import dumps, loads
+
+
+DEFAULT_DATA_TABLE_NAMES = ["mentalist_databases"]
+
+
+def mentalist_download_pubmlst( data_manager_dict, kmer_size, scheme, params, target_directory, data_table_names=DEFAULT_DATA_TABLE_NAMES ):
+ translation_table = string.maketrans(string.punctuation, ("_" * 32))
+ base_path = scheme.lower().replace(" ", "_").translate(translation_table) + "_pubmlst"
+ today = datetime.date.today().isoformat()
+ scheme_files_path = base_path + "_scheme_" + today
+ database_path = base_path + "_k" + str(kmer_size) + "_" + today
+ database_name = base_path + "_k" + str(kmer_size) + "_" + today + ".jld"
+ display_name = scheme + " k=" + str(kmer_size) + " (PubMLST) " + today
+ args = [ 'mentalist', 'download_pubmlst', '-s', scheme, '-k', str(kmer_size), '--db', database_name, '-o', scheme_files_path]
+ proc = subprocess.Popen( args=args, shell=False, cwd=target_directory )
+ return_code = proc.wait()
+ if return_code:
+ print("Error building database.", file=sys.stderr)
+ sys.exit( return_code )
+ data_table_entry = dict( value=database_path, dbkey='PubMLST', name=display_name, path=database_name )
+ for data_table_name in data_table_names:
+ _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( '-s', '--scheme', dest='scheme', default=None, help='Scheme' )
+ parser.add_argument( '-k', '--kmer_size', dest='kmer_size', type=int, default=None, help='kmer Size' )
+ args = parser.parse_args()
+
+ params = 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
+ mentalist_download_pubmlst( data_manager_dict, args.kmer_size, args.scheme, params, target_directory, DEFAULT_DATA_TABLE_NAMES )
+
+ # save info to json file
+ open( args.params, 'wb' ).write( dumps( data_manager_dict ) )
+
+
+if __name__ == "__main__":
+ main()
diff -r 000000000000 -r 1d9e3950ce61 data_managers/data_manager_mentalist_download_pubmlst/data_manager/mentalist_download_pubmlst.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_managers/data_manager_mentalist_download_pubmlst/data_manager/mentalist_download_pubmlst.xml Wed Dec 20 17:36:03 2017 -0500
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diff -r 000000000000 -r 1d9e3950ce61 data_managers/data_manager_mentalist_download_pubmlst/tool-data/mentalist_databases.loc.sample
diff -r 000000000000 -r 1d9e3950ce61 data_managers/data_manager_mentalist_download_pubmlst/tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_managers/data_manager_mentalist_download_pubmlst/tool_data_table_conf.xml.sample Wed Dec 20 17:36:03 2017 -0500
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\ No newline at end of file
diff -r 000000000000 -r 1d9e3950ce61 tools/mentalist_call/mentalist_call.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/mentalist_call/mentalist_call.xml Wed Dec 20 17:36:03 2017 -0500
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