# HG changeset patch
# User iuc
# Date 1618865646 0
# Node ID 169b08c9713c5851bff230d58f9f7750b3e485c1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_metaphlan_database_downloader commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
diff -r 000000000000 -r 169b08c9713c data_manager/data_manager_metaphlan_download.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/data_manager_metaphlan_download.py Mon Apr 19 20:54:06 2021 +0000
@@ -0,0 +1,146 @@
+#!/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_metaphlan_db(data_tables, index, table_name, target_dp):
+ """Download MetaPhlAn database
+
+ 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
+ index: version
+ table_name: name of the table
+ target_dp: directory to put copy or link to the data file
+
+ """
+ db_dp = target_dp / Path(index)
+ cmd = "metaphlan --install --index %s --bowtie2db %s" % (index, db_dp)
+ subprocess.check_call(cmd, shell=True)
+ add_data_table_entry(
+ data_tables,
+ table_name,
+ dict(
+ dbkey=index,
+ value='%s-%s' % (index, date.today().strftime("%d%m%Y")),
+ name="MetaPhlAn clade-specific marker genes (%s)" % index,
+ path=str(db_dp)))
+
+
+if __name__ == "__main__":
+ print("Starting...")
+
+ # Read command line
+ parser = argparse.ArgumentParser(description='Download and build MetaPhlan database')
+ parser.add_argument('--index', help="Version of the database")
+ parser.add_argument('--json', help="Path to JSON file")
+ 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, "metaphlan_database")
+
+ # Fetch data from specified data sources
+ print("Download and build database")
+ download_metaphlan_db(
+ data_tables,
+ args.index,
+ "metaphlan_database",
+ target_dp)
+
+ # 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 169b08c9713c data_manager/data_manager_metaphlan_download.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/data_manager_metaphlan_download.xml Mon Apr 19 20:54:06 2021 +0000
@@ -0,0 +1,36 @@
+
+
+
+ metaphlan
+
+
+ 3.0.7
+ 0
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ 1101/2020.11.19.388223
+
+
+
diff -r 000000000000 -r 169b08c9713c data_manager_conf.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager_conf.xml Mon Apr 19 20:54:06 2021 +0000
@@ -0,0 +1,21 @@
+
+
+
+
+
+
+
+
+
diff -r 000000000000 -r 169b08c9713c tool-data/metaphlan_database.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/metaphlan_database.loc.sample Mon Apr 19 20:54:06 2021 +0000
@@ -0,0 +1,4 @@
+#This is a sample file distributed with Galaxy that enables tools
+#to use a directory of metagenomics files.
+#file has this format (white space characters are TAB characters)
+#02_16_2014 MetaPhlAn2 clade-specific marker genes db_v20 /path/to/data
diff -r 000000000000 -r 169b08c9713c tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample Mon Apr 19 20:54:06 2021 +0000
@@ -0,0 +1,6 @@
+
+