# HG changeset patch
# User dfornika
# Date 1507330973 14400
# Node ID 0f74aa0cfb682b05e004d00625155ea0d315993c
# Parent a0a6d3e7416d30d5cac2d07003893938117d1609
planemo upload for repository https://github.com/WGS-TB/MentaLiST/tree/master/galaxy
diff -r a0a6d3e7416d -r 0f74aa0cfb68 README
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/README Fri Oct 06 19:02:53 2017 -0400
@@ -0,0 +1,1 @@
+TODO: Fill in README file.
\ No newline at end of file
diff -r a0a6d3e7416d -r 0f74aa0cfb68 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 Fri Oct 06 19:02:53 2017 -0400
@@ -0,0 +1,67 @@
+#!/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 build_mentalist_database( 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 + '/' + 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='fasta_filenames' )
+ 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='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
+ build_mentalist_database( 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 a0a6d3e7416d -r 0f74aa0cfb68 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 Fri Oct 06 19:02:53 2017 -0400
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+
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+ mentalist
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+ 10.1101/172858
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diff -r a0a6d3e7416d -r 0f74aa0cfb68 data_managers/data_manager_mentalist_build_db/data_manager_conf.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_managers/data_manager_mentalist_build_db/data_manager_conf.xml Fri Oct 06 19:02:53 2017 -0400
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diff -r a0a6d3e7416d -r 0f74aa0cfb68 data_managers/data_manager_mentalist_build_db/tool-data/mentalist_databases.loc.sample
diff -r a0a6d3e7416d -r 0f74aa0cfb68 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 Fri Oct 06 19:02:53 2017 -0400
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diff -r a0a6d3e7416d -r 0f74aa0cfb68 data_managers/data_manager_mentalist_download_cgmlst/data_manager/make_json.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_managers/data_manager_mentalist_download_cgmlst/data_manager/make_json.py Fri Oct 06 19:02:53 2017 -0400
@@ -0,0 +1,27 @@
+import argparse
+import json
+import os
+import shutil
+
+
+def main(args):
+ data_manager_entry = {}
+ data_manager_entry['value'] = args.database.lower()
+ data_manager_entry['name'] = args.database
+ data_manager_entry['path'] = '.'
+ data_manager_json = dict(data_tables = dict(mentalist_databases = data_manager_entry))
+ params = json.loads(open(args.output).read())
+ target_directory = params['output_data'][0]['extra_files_path']
+ os.mkdir(target_directory)
+ output_path = os.path.join(os.getcwd(), 'mentalist-database/cgmlst')
+ for filename in os.listdir(output_path):
+ shutil.move(os.path.join(output_path, filename), target_directory)
+ file(args.output, 'w').write(json.dumps(data_manager_json))
+
+
+if __name__ == '__main__':
+ parser = argparse.ArgumentParser(description='Create data manager json.')
+ parser.add_argument('--db', dest='database', action='store', help='Database name')
+ parser.add_argument('--out', dest='output', action='store', help='JSON filename')
+ args = parser.parse_args()
+ main(args)
diff -r a0a6d3e7416d -r 0f74aa0cfb68 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 Fri Oct 06 19:02:53 2017 -0400
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+
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+ 10.1101/172858
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diff -r a0a6d3e7416d -r 0f74aa0cfb68 data_managers/data_manager_mentalist_download_cgmlst/data_manager_conf.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_managers/data_manager_mentalist_download_cgmlst/data_manager_conf.xml Fri Oct 06 19:02:53 2017 -0400
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diff -r a0a6d3e7416d -r 0f74aa0cfb68 data_managers/data_manager_mentalist_download_cgmlst/tool-data/mentalist_databases.loc.sample
diff -r a0a6d3e7416d -r 0f74aa0cfb68 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 Fri Oct 06 19:02:53 2017 -0400
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diff -r a0a6d3e7416d -r 0f74aa0cfb68 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 Fri Oct 06 19:02:53 2017 -0400
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+ 10.1101/172858
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diff -r a0a6d3e7416d -r 0f74aa0cfb68 data_managers/data_manager_mentalist_download_pubmlst/data_manager_conf.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_managers/data_manager_mentalist_download_pubmlst/data_manager_conf.xml Fri Oct 06 19:02:53 2017 -0400
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diff -r a0a6d3e7416d -r 0f74aa0cfb68 data_managers/data_manager_mentalist_download_pubmlst/tool-data/mentalist_databases.loc.sample
diff -r a0a6d3e7416d -r 0f74aa0cfb68 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 Fri Oct 06 19:02:53 2017 -0400
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diff -r a0a6d3e7416d -r 0f74aa0cfb68 tools/mentalist_build.xml
--- a/tools/mentalist_build.xml Thu Sep 14 17:16:16 2017 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,33 +0,0 @@
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diff -r a0a6d3e7416d -r 0f74aa0cfb68 tools/mentalist_call.xml
--- a/tools/mentalist_call.xml Thu Sep 14 17:16:16 2017 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,72 +0,0 @@
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diff -r a0a6d3e7416d -r 0f74aa0cfb68 tools/mentalist_call/mentalist_call.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/mentalist_call/mentalist_call.xml Fri Oct 06 19:02:53 2017 -0400
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+
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