# HG changeset patch
# User dfornika
# Date 1507661974 14400
# Node ID 01319da48668ab99e5c725664ada3e86857586df
# Parent d23b89e71ee545f0f811a637b2ba9cd55e5495a4
planemo upload for repository https://github.com/WGS-TB/MentaLiST/tree/master/galaxy commit 6b0c89e9bbaa49824c75326cde4c896b6ac07482-dirty
diff -r d23b89e71ee5 -r 01319da48668 data_managers/data_manager_mentalist_build_db/data_manager/mentalist_build_db.py
--- a/data_managers/data_manager_mentalist_build_db/data_manager/mentalist_build_db.py Fri Oct 06 19:05:19 2017 -0400
+++ b/data_managers/data_manager_mentalist_build_db/data_manager/mentalist_build_db.py Tue Oct 10 14:59:34 2017 -0400
@@ -11,7 +11,7 @@
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 ):
+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]
@@ -37,10 +37,10 @@
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' )
+ 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() )
@@ -57,7 +57,7 @@
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 )
+ 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 ) )
diff -r d23b89e71ee5 -r 01319da48668 data_managers/data_manager_mentalist_download_cgmlst/data_manager/mentalist_download_cgmlst.xml
--- a/data_managers/data_manager_mentalist_download_cgmlst/data_manager/mentalist_download_cgmlst.xml Fri Oct 06 19:05:19 2017 -0400
+++ b/data_managers/data_manager_mentalist_download_cgmlst/data_manager/mentalist_download_cgmlst.xml Tue Oct 10 14:59:34 2017 -0400
@@ -5,28 +5,28 @@
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diff -r d23b89e71ee5 -r 01319da48668 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 Tue Oct 10 14:59:34 2017 -0400
@@ -0,0 +1,63 @@
+#!/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_download_cgmlst( data_manager_dict, database_name, kmer_size, scheme, output, params, target_directory, data_table_names=DEFAULT_DATA_TABLE_NAMES ):
+ args = [ 'mentalist', 'download_pubmlst', '--db', database_name, '-k', str(kmer_size), '-s', scheme, '-o' output]
+ 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='Database Name' )
+ 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' )
+ parser.add_argument( '-o', '--output', dest='output', default=None, help='Output' )
+ 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.database_name, args.kmer_size, args.scheme, args.output, 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 d23b89e71ee5 -r 01319da48668 data_managers/data_manager_mentalist_download_pubmlst/data_manager/mentalist_download_pubmlst.xml
--- a/data_managers/data_manager_mentalist_download_pubmlst/data_manager/mentalist_download_pubmlst.xml Fri Oct 06 19:05:19 2017 -0400
+++ b/data_managers/data_manager_mentalist_download_pubmlst/data_manager/mentalist_download_pubmlst.xml Tue Oct 10 14:59:34 2017 -0400
@@ -5,21 +5,154 @@
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