# HG changeset patch
# User greg
# Date 1666125448 0
# Node ID 53652e89e4151bce4128b729c1990d611218a613
Uploaded
diff -r 000000000000 -r 53652e89e415 .shed.yml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/.shed.yml Tue Oct 18 20:37:28 2022 +0000
@@ -0,0 +1,13 @@
+name: data_manager_pima_pv_downloader
+owner: iuc
+description: Data manager to download the PIMA plasmids_and_vectors.fasta files for use by the PIMA pipeline tools.
+homepage_url: https://github.com/appliedbinf/pima_md
+long_description: |
+ PIMA (Plasmid, Integrations, Mutations, and Antibiotic) resistance annotation pipeline is a high-throughput
+ sequence analysis pipeline. PIMA is an end-to-end solution encompassing all the steps required to transform
+ raw ONT output into high-quality annotated assemblies. PIMA supports providing optional Illumina paired end
+ reads for polishing and error correcting assemblies.
+remote_repository_url: "https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pima_pv_downloader"
+type: unrestricted
+categories:
+- Data Managers
diff -r 000000000000 -r 53652e89e415 data_manager/pima_pv_downloader.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/pima_pv_downloader.py Tue Oct 18 20:37:28 2022 +0000
@@ -0,0 +1,62 @@
+import argparse
+import datetime
+import json
+import os
+import sys
+
+from urllib.request import Request, urlopen
+
+
+def url_download(url, workdir):
+ file_path = os.path.abspath(os.path.join(workdir, os.path.basename(url)))
+ src = None
+ dst = None
+ try:
+ req = Request(url)
+ src = urlopen(req)
+ with open(file_path, 'wb') as dst:
+ while True:
+ chunk = src.read(2**10)
+ if chunk:
+ dst.write(chunk)
+ else:
+ break
+ except Exception as e:
+ sys.exit(str(e))
+ finally:
+ if src:
+ src.close()
+ return file_path
+
+
+def download(url, out_file):
+ today = datetime.datetime.utcnow().strftime("%Y-%m-%d")
+
+ with open(out_file) as fh:
+ params = json.load(fh)
+
+ workdir = params['output_data'][0]['extra_files_path']
+ os.makedirs(workdir)
+ file_path = url_download(url, workdir)
+ value = '%s_pima_plasmids_and_values' % today
+ name = '%s %s' % (today, os.path.basename(file_path))
+
+ data_manager_json = {"data_tables": {}}
+ data_manager_entry = {}
+ data_manager_entry['value'] = value
+ data_manager_entry['name'] = name
+ data_manager_entry['path'] = file_path
+ data_manager_json["data_tables"]["vsnp_genbank"] = data_manager_entry
+
+ with open(out_file, 'w') as fh:
+ json.dump(data_manager_json, fh, sort_keys=True)
+
+
+parser = argparse.ArgumentParser()
+
+parser.add_argument('--url', dest='url', help='URL to download plasmids_and_vectors.fasta file')
+parser.add_argument('--out_file', dest='out_file', help='JSON output file')
+
+args = parser.parse_args()
+
+download(args.url, args.out_file)
diff -r 000000000000 -r 53652e89e415 data_manager/pima_pv_downloader.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/pima_pv_downloader.xml Tue Oct 18 20:37:28 2022 +0000
@@ -0,0 +1,30 @@
+
+ Download plasmids_and_vectors.fasta files
+
+ python
+
+
+
+
+
+
+
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+
+
+
+
+
+
+
+
+
+ 10.1038/s41598-019-49700-1
+
+
diff -r 000000000000 -r 53652e89e415 data_manager_conf.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager_conf.xml Tue Oct 18 20:37:28 2022 +0000
@@ -0,0 +1,20 @@
+
+
+
+
+
+
+
+
+
diff -r 000000000000 -r 53652e89e415 test-data/pima_pv.json
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pima_pv.json Tue Oct 18 20:37:28 2022 +0000
@@ -0,0 +1,1 @@
+{"data_tables": {"pima_pv":
diff -r 000000000000 -r 53652e89e415 test-data/pima_pv.loc
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/pima_pv.loc Tue Oct 18 20:37:28 2022 +0000
@@ -0,0 +1,12 @@
+# This is a sample file distributed with Galaxy that enables tools
+# to use a selected PIMA plasmids_and_vectors.fasta file. The pima_pv.loc
+# file has this format (longer white space characters are TAB characters):
+#
+#
+#
+# So, for example, if you have the plasmids_and_vectors.fasta files stored in
+# /depot/data2/galaxy/pima_pv/,
+# then the pima_pv.loc entry would look like this:
+#
+# 2022-10-18 PIMA plasmids_and_vectors.fasta /depot/data2/galaxy/pima_pv
+2022-10-18 2022-10-18 plasmids_and_vectors.fasta ${__HERE__}
diff -r 000000000000 -r 53652e89e415 tool-data/pima_pv.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/pima_pv.loc.sample Tue Oct 18 20:37:28 2022 +0000
@@ -0,0 +1,3 @@
+## PIMA plasmids_and_vectors.fasta files
+#Value Name Path
+#2022-10-18 plasmids_and_vectors.fasta (2022-10-18) /depot/data2/galaxy/tool-data/pima_pv/2022-10-18
diff -r 000000000000 -r 53652e89e415 tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample Tue Oct 18 20:37:28 2022 +0000
@@ -0,0 +1,8 @@
+
+
+
+
+
diff -r 000000000000 -r 53652e89e415 tool_data_table_conf.xml.test
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.test Tue Oct 18 20:37:28 2022 +0000
@@ -0,0 +1,7 @@
+
+
+
+