# HG changeset patch
# User iuc
# Date 1665783175 0
# Node ID 676915c44e1e3c96fc61de69cfaac4a8937df65e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
diff -r 000000000000 -r 676915c44e1e data_manager/data_manager_semibin.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/data_manager_semibin.py Fri Oct 14 21:32:55 2022 +0000
@@ -0,0 +1,153 @@
+#!/usr/bin/env python
+#
+# Data manager for reference data for the MetaPhlAn Galaxy tools
+import argparse
+import json
+import subprocess
+from datetime import date
+from pathlib import Path
+
+
+# Utility functions for interacting with Galaxy JSON
+def read_input_json(json_fp):
+ """Read the JSON supplied from the data manager tool
+
+ Returns a tuple (param_dict,extra_files_path)
+
+ 'param_dict' is an arbitrary dictionary of parameters
+ input into the tool; 'extra_files_path' is the path
+ to a directory where output files must be put for the
+ receiving data manager to pick them up.
+
+ NB the directory pointed to by 'extra_files_path'
+ doesn't exist initially, it is the job of the script
+ to create it if necessary.
+
+ """
+ with open(json_fp) as fh:
+ params = json.load(fh)
+ return (params['param_dict'],
+ Path(params['output_data'][0]['extra_files_path']))
+
+
+# Utility functions for creating data table dictionaries
+#
+# Example usage:
+# >>> d = create_data_tables_dict()
+# >>> add_data_table(d,'my_data')
+# >>> add_data_table_entry(dict(dbkey='hg19',value='human'))
+# >>> add_data_table_entry(dict(dbkey='mm9',value='mouse'))
+# >>> print(json.dumps(d))
+def create_data_tables_dict():
+ """Return a dictionary for storing data table information
+
+ Returns a dictionary that can be used with 'add_data_table'
+ and 'add_data_table_entry' to store information about a
+ data table. It can be converted to JSON to be sent back to
+ the data manager.
+
+ """
+ d = {
+ 'data_tables': {}
+ }
+ return d
+
+
+def add_data_table(d, table):
+ """Add a data table to the data tables dictionary
+
+ Creates a placeholder for a data table called 'table'.
+
+ """
+ d['data_tables'][table] = []
+
+
+def add_data_table_entry(d, table, entry):
+ """Add an entry to a data table
+
+ Appends an entry to the data table 'table'. 'entry'
+ should be a dictionary where the keys are the names of
+ columns in the data table.
+
+ Raises an exception if the named data table doesn't
+ exist.
+
+ """
+ try:
+ d['data_tables'][table].append(entry)
+ except KeyError:
+ raise Exception("add_data_table_entry: no table '%s'" % table)
+
+
+def download_gtdb(data_tables, table_name, target_dp, test=False):
+ """Download GTDB
+
+ Creates references to the specified file(s) on the Galaxy
+ server in the appropriate data table (determined from the
+ file extension).
+
+ The 'data_tables' dictionary should have been created using
+ the 'create_data_tables_dict' and 'add_data_table' functions.
+
+ Arguments:
+ data_tables: a dictionary containing the data table info
+ table_name: name of the table
+ target_dp: directory to put copy or link to the data file
+
+ """
+ db_dp = target_dp
+ if not test:
+ cmd = "SemiBin download_GTDB --reference-db-data-dir %s" % (db_dp)
+ subprocess.check_call(cmd, shell=True)
+ dbkey = 'gtdb'
+ name = "GTDB reference genome generated by MMseqs2 used in SemiBin"
+ else:
+ dbkey = 'test'
+ name = "Test"
+ empty_fp = db_dp / Path("empty")
+ empty_fp.touch()
+ add_data_table_entry(
+ data_tables,
+ table_name,
+ dict(
+ dbkey=dbkey,
+ value='%s' % (date.today().strftime("%d%m%Y")),
+ name=name,
+ path=str(db_dp)))
+
+
+if __name__ == "__main__":
+ print("Starting...")
+
+ # Read command line
+ parser = argparse.ArgumentParser(description='Download reference genomes (GTDB)')
+ parser.add_argument('--json', help="Path to JSON file")
+ parser.add_argument('--test', action='store_true', help="Test")
+ args = parser.parse_args()
+ print("args : %s" % args)
+
+ # Read the input JSON
+ json_fp = Path(args.json)
+ params, target_dp = read_input_json(json_fp)
+
+ # Make the target directory
+ print("Making %s" % target_dp)
+ target_dp.mkdir(parents=True, exist_ok=True)
+
+ # Set up data tables dictionary
+ data_tables = create_data_tables_dict()
+ add_data_table(data_tables, "gtdb")
+
+ # Fetch data from specified data sources
+ print("Download and build database")
+ download_gtdb(
+ data_tables,
+ "gtdb",
+ target_dp,
+ args.test)
+
+ # Write output JSON
+ print("Outputting JSON")
+ with open(json_fp, 'w') as fh:
+ json.dump(data_tables, fh, sort_keys=True)
+ print("Done.")
diff -r 000000000000 -r 676915c44e1e data_manager/data_manager_semibin.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/data_manager_semibin.xml Fri Oct 14 21:32:55 2022 +0000
@@ -0,0 +1,39 @@
+
+
+
+ semibin
+
+
+ 1.1.1
+ 0
+ 21.01
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ 10.1038/s41467-022-29843-y
+
+
diff -r 000000000000 -r 676915c44e1e data_manager_conf.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager_conf.xml Fri Oct 14 21:32:55 2022 +0000
@@ -0,0 +1,21 @@
+
+
+
+
+
+
+
+
+
diff -r 000000000000 -r 676915c44e1e test-data/gtdb.loc
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gtdb.loc Fri Oct 14 21:32:55 2022 +0000
@@ -0,0 +1,3 @@
+#file has this format (white space characters are TAB characters)
+#dbkey description name /path/to/data
+test-date description test /path/to/data
\ No newline at end of file
diff -r 000000000000 -r 676915c44e1e tool-data/gtdb.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/gtdb.loc.sample Fri Oct 14 21:32:55 2022 +0000
@@ -0,0 +1,2 @@
+#file has this format (white space characters are TAB characters)
+#dbkey description name /path/to/data
diff -r 000000000000 -r 676915c44e1e tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample Fri Oct 14 21:32:55 2022 +0000
@@ -0,0 +1,6 @@
+
+