# HG changeset patch
# User bebatut
# Date 1487668633 18000
# Node ID 1a5151add645f06ecf8486a67e14cbe2289c5032
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/data_managers/data_manager_metaphlan2_database_downloader commit d474c6ecde051fa66db3635ba28bbbf28623cfdc-dirty
diff -r 000000000000 -r 1a5151add645 data_manager/data_manager_metaphlan2_download.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/data_manager_metaphlan2_download.py Tue Feb 21 04:17:13 2017 -0500
@@ -0,0 +1,150 @@
+#!/usr/bin/env python
+#
+# Data manager for reference data for the 'humann2' Galaxy tools
+import datetime
+import json
+import optparse
+import os
+import subprocess
+import sys
+
+
+# Utility functions for interacting with Galaxy JSON
+def read_input_json(jsonfile):
+ """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.
+
+ """
+ params = json.loads(open(jsonfile).read())
+ return (params['param_dict'],
+ 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 str(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 = {}
+ 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_metaphlan2_db(data_tables, table_name, target_dir):
+ """Download MetaPhlAn2 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
+ table_name: name of the table
+ target_dir: directory to put copy or link to the data file
+
+ """
+ today = datetime.date.today()
+ db_target_dir = os.path.join(target_dir, database, build)
+ os.makedirs(db_target_dir)
+ cmd = "metaphlan2_databases --output %s" % (db_target_dir)
+ subprocess.check_call(cmd, shell=True)
+ add_data_table_entry(
+ data_tables,
+ table_name,
+ dict(
+ dbkey="db_v20",
+ value=today.isoformat(),
+ name="MetaPhlAn2 clade-specific marker genes")
+
+
+if __name__ == "__main__":
+ print("Starting...")
+
+ # Read command line
+ parser = optparse.OptionParser(description='Download MetaPhlan2 database')
+ parser.add_option('--database', help="Database name")
+ options, args = parser.parse_args()
+ print("args : %s" % args)
+
+
+ # Check for JSON file
+ if len(args) != 1:
+ sys.stderr.write("Need to supply JSON file name")
+ sys.exit(1)
+
+ jsonfile = args[0]
+
+ # Read the input JSON
+ params, target_dir = read_input_json(jsonfile)
+
+ # Make the target directory
+ print("Making %s" % target_dir)
+ os.mkdir(target_dir)
+
+ # Set up data tables dictionary
+ data_tables = create_data_tables_dict()
+ add_data_table(data_tables, "metaphlan2_database")
+
+ # Fetch data from specified data sources
+ if options.database == "db_v20":
+ download_metaphlan2_db(
+ data_tables,
+ "metaphlan2_database",
+ target_dir)
+
+ # Write output JSON
+ print("Outputting JSON")
+ print(str(json.dumps(data_tables)))
+ open(jsonfile, 'wb').write(json.dumps(data_tables))
+ print("Done.")
diff -r 000000000000 -r 1a5151add645 data_manager/data_manager_metaphlan2_download.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/data_manager_metaphlan2_download.xml Tue Feb 21 04:17:13 2017 -0500
@@ -0,0 +1,40 @@
+
+ Download MetaPhlAn2 database
+
+
+ metaphlan2
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ 10.1371/journal.pcbi.1003153
+
+
+
diff -r 000000000000 -r 1a5151add645 data_manager_conf.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager_conf.xml Tue Feb 21 04:17:13 2017 -0500
@@ -0,0 +1,20 @@
+
+
+
+
+
+
+
+
+
diff -r 000000000000 -r 1a5151add645 shed.yml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/shed.yml Tue Feb 21 04:17:13 2017 -0500
@@ -0,0 +1,13 @@
+name: data_manager_metaphlan2_database_downloader
+owner: bebatut
+description: "MetaPhlAn for Metagenomic Phylogenetic Analysis"
+homepage_url: "https://bitbucket.org/biobakery/metaphlan2/"
+long_description: |
+ MetaPhlAn is a computational tool for profiling the composition of microbial
+ communities (Bacteria, Archaea, Eukaryotes and Viruses) from metagenomic shotgun
+ sequencing data with species level resolution
+remote_repository_url: "https://github.com/ASaiM/galaxytools/tree/master/data_managers/data_manager_metaphlan2_database_downloader"
+type: unrestricted
+categories:
+- Metagenomics
+- Data Managers
\ No newline at end of file
diff -r 000000000000 -r 1a5151add645 tool-data/metaphlan2_database.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/metaphlan2_database.loc.sample Tue Feb 21 04:17:13 2017 -0500
@@ -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
\ No newline at end of file
diff -r 000000000000 -r 1a5151add645 tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample Tue Feb 21 04:17:13 2017 -0500
@@ -0,0 +1,6 @@
+
+