# HG changeset patch
# User iuc
# Date 1662052567 0
# Node ID bd342a6a5b0f0f24f37900ec36174e9d11fb3a0c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dram_database_downloader commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
diff -r 000000000000 -r bd342a6a5b0f data_manager/data_manager_dram_download.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/data_manager_dram_download.py Thu Sep 01 17:16:07 2022 +0000
@@ -0,0 +1,93 @@
+#!/usr/bin/env python
+
+import argparse
+import json
+import os
+import subprocess
+
+
+parser = argparse.ArgumentParser()
+
+parser.add_argument('--kofam_hmm_loc', action='store', dest='kofam_hmm_loc', default=None, help='hmm file for KOfam')
+parser.add_argument('--kofam_ko_list_loc', action='store', dest='kofam_ko_list_loc', default=None, help='KOfam ko list file')
+parser.add_argument('--skip_uniref', action='store', dest='skip_uniref', default='no', help='Flag to Download and process uniref')
+parser.add_argument('--uniref_loc', action='store', dest='uniref_loc', default=None, help='uniref file')
+parser.add_argument('--uniref_version', action='store', dest='uniref_version', type=int, default=90, help='uniref version to download')
+parser.add_argument('--pfam_loc', action='store', dest='pfam_loc', default=None, help='pfam-A full file')
+parser.add_argument('--pfam_hmm_dat', action='store', dest='pfam_hmm_dat', help='pfam hmm .dat file to get PF descriptions')
+parser.add_argument('--dbcan_loc', action='store', dest='dbcan_loc', default=None, help='dbCAN file')
+parser.add_argument('--dbcan_fam_activities', action='store', dest='dbcan_fam_activities', default=None, help='CAZY family activities file')
+parser.add_argument('--dbcan_version', action='store', dest='dbcan_version', type=int, default=10, help='Version of dbCAN to use')
+parser.add_argument('--vogdb_loc', action='store', dest='vogdb_loc', default=None, help='hmm file for vogdb')
+parser.add_argument('--vog_annotations', action='store', dest='vog_annotations', default=None, help='vogdb annotations file')
+parser.add_argument('--viral_loc', action='store', dest='viral_loc', default=None, help='merged viral protein faa file')
+parser.add_argument('--peptidase_loc', action='store', dest='peptidase_loc', default=None, help='MEROPS peptidase fasta file')
+parser.add_argument('--genome_summary_form_loc', action='store', dest='genome_summary_form_loc', default=None, help='genome summary form file')
+parser.add_argument('--module_step_form_loc', action='store', dest='module_step_form_loc', default=None, help='module step form file')
+parser.add_argument('--etc_module_database_loc', action='store', dest='etc_module_database_loc', default=None, help='etc module database file')
+parser.add_argument('--function_heatmap_form_loc', action='store', dest='function_heatmap_form_loc', default=None, help='function heatmap form file')
+parser.add_argument('--amg_database_loc', action='store', dest='amg_database_loc', default=None, help='amg database file')
+parser.add_argument('--db_version', action='store', dest='db_version', help='Version of DRAM databases')
+parser.add_argument('--threads', action='store', dest='threads', type=int, help='Number of processes')
+parser.add_argument('--out_file', action='store', dest='out_file', help='JSON output file')
+
+args = parser.parse_args()
+
+with open(args.out_file) as fh:
+ params = json.load(fh)
+
+target_directory = params['output_data'][0]['extra_files_path']
+os.makedirs(target_directory)
+
+# Download the data.
+cmd = 'DRAM-setup.py prepare_databases --output_dir %s' % target_directory
+if args.kofam_hmm_loc is not None:
+ cmd = '%s --kofam_hmm_loc %s' % (cmd, args.kofam_hmm_loc)
+if args.kofam_ko_list_loc is not None:
+ cmd = '%s --kofam_ko_list_loc %s' % (cmd, args.kofam_ko_list_loc)
+if args.skip_uniref == 'yes':
+ cmd = '%s --skip_uniref' % cmd
+else:
+ if args.uniref_loc is not None:
+ cmd = '%s --uniref_loc %s' % (cmd, args.uniref_loc)
+ cmd = '%s --uniref_version %d' % (cmd, args.uniref_version)
+if args.pfam_loc is not None:
+ cmd = '%s --pfam_loc %s' % (cmd, args.pfam_loc)
+if args.pfam_hmm_dat is not None:
+ cmd = '%s --pfam_hmm_dat %s' % (cmd, args.pfam_hmm_dat)
+if args.dbcan_loc is not None:
+ cmd = '%s --dbcan_loc %s' % (cmd, args.dbcan_loc)
+if args.dbcan_fam_activities is not None:
+ cmd = '%s --dbcan_fam_activities %s' % (cmd, args.dbcan_fam_activities)
+cmd = '%s --dbcan_version %d' % (cmd, args.dbcan_version)
+if args.vogdb_loc is not None:
+ cmd = '%s --vogdb_loc %s' % (cmd, args.vogdb_loc)
+if args.vog_annotations is not None:
+ cmd = '%s --vog_annotations %s' % (cmd, args.vog_annotations)
+if args.viral_loc is not None:
+ cmd = '%s --viral_loc %s' % (cmd, args.viral_loc)
+if args.peptidase_loc is not None:
+ cmd = '%s --peptidase_loc %s' % (cmd, args.peptidase_loc)
+if args.genome_summary_form_loc is not None:
+ cmd = '%s --genome_summary_form_loc %s' % (cmd, args.genome_summary_form_loc)
+if args.module_step_form_loc is not None:
+ cmd = '%s --module_step_form_loc %s' % (cmd, args.module_step_form_loc)
+if args.etc_module_database_loc is not None:
+ cmd = '%s --etc_module_database_loc %s' % (cmd, args.etc_module_database_loc)
+if args.function_heatmap_form_loc is not None:
+ cmd = '%s --function_heatmap_form_loc %s' % (cmd, args.function_heatmap_form_loc)
+if args.amg_database_loc is not None:
+ cmd = '%s --amg_database_loc %s' % (cmd, args.amg_database_loc)
+cmd = '%s --threads %d' % (cmd, args.threads)
+
+subprocess.check_call(cmd, shell=True)
+
+data_manager_json = {'data_tables': {}}
+data_manager_entry = {}
+data_manager_entry['value'] = args.db_version
+data_manager_entry['name'] = 'DRAM %s databases' % args.db_version
+data_manager_entry['path'] = target_directory
+data_manager_json['data_tables']['dram_databases'] = data_manager_entry
+
+with open(args.out_file, 'w') as fh:
+ json.dump(data_manager_json, fh, sort_keys=True)
diff -r 000000000000 -r bd342a6a5b0f data_manager/data_manager_dram_download.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/data_manager_dram_download.xml Thu Sep 01 17:16:07 2022 +0000
@@ -0,0 +1,235 @@
+
+ required by the DRAM suite of tools
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+ dram
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+This tool downloads and processes DRAM databases for annotation and makes them available to corresponding versions
+of the DRAM suite of tools.
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+See https://github.com/WrightonLabCSU/DRAM/wiki for details about DRAM.
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+ 10.1093/nar/gkaa621
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diff -r 000000000000 -r bd342a6a5b0f data_manager_conf.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager_conf.xml Thu Sep 01 17:16:07 2022 +0000
@@ -0,0 +1,19 @@
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diff -r 000000000000 -r bd342a6a5b0f test-data/dram_databases.loc
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/dram_databases.loc Thu Sep 01 17:16:07 2022 +0000
@@ -0,0 +1,12 @@
+# This is a sample file distributed with Galaxy that enables tools
+# to use a directory of DRAM databases. The dram_databases.loc
+# file has this format (longer white space characters are TAB characters):
+#
+#
+#
+# So, for example, if you have the DRAM databases stored in
+# /depot/data2/galaxy/dram/,
+# then the gtdbtk_databases.loc entry would look like this:
+#
+# 3.5.1 DRAM database /depot/data2/galaxy/dram
+3.5.1 DRAM 3.5.1 databases ${__HERE__}
diff -r 000000000000 -r bd342a6a5b0f tool-data/dram_databases.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/dram_databases.loc.sample Thu Sep 01 17:16:07 2022 +0000
@@ -0,0 +1,3 @@
+## DRAM databases
+#Value Name Path
+#2022-07-04 DRAM annotations (2022-07-04) /depot/data2/galaxy/tool-data/dram_databases/2022-07-04
diff -r 000000000000 -r bd342a6a5b0f tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample Thu Sep 01 17:16:07 2022 +0000
@@ -0,0 +1,8 @@
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diff -r 000000000000 -r bd342a6a5b0f tool_data_table_conf.xml.test
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.test Thu Sep 01 17:16:07 2022 +0000
@@ -0,0 +1,7 @@
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