# HG changeset patch
# User iuc
# Date 1723650158 0
# Node ID d28438704310c4a2b26add2a80f1c01f6ec980ce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_omamer commit b890cd87ef5cfaa81eda29cc935de224ecb05bb6
diff -r 000000000000 -r d28438704310 data_manager/macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/macros.xml Wed Aug 14 15:42:38 2024 +0000
@@ -0,0 +1,12 @@
+
+
+ 2.0.2
+ 2
+
+
+
+ python
+ requests
+
+
+
diff -r 000000000000 -r d28438704310 data_manager/omamer.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/omamer.py Wed Aug 14 15:42:38 2024 +0000
@@ -0,0 +1,86 @@
+#!/usr/bin/env python
+
+import argparse
+import json
+import os
+import sys
+
+import requests
+
+# URL for downloading OMAmer datasets
+OMAMER_DATASETS_URL = "https://omabrowser.org/All/{dataset}"
+
+# List of OMAmer data sets with versions
+OMAMER_DATASETS = {
+ "Primates_v2.0.0": "Primates-v2.0.0.h5",
+ "Viridiplantae_v2.0.0": "Viridiplantae-v2.0.0.h5",
+ "Metazoa_v2.0.0": "Metazoa-v2.0.0.h5",
+ "LUCA_v0.2.5": "LUCA-v0.2.5.h5",
+ "LUCA_v2.0.0": "LUCA-v2.0.0.h5",
+ "Saccharomyceta": "Saccharomyceta.h5",
+ "Homininae": "Homininae.h5",
+}
+
+DEFAULT_OUTPUT_DIR = "database_omamer"
+
+
+def download_file(url, dest):
+ try:
+ with requests.get(url, stream=True) as r:
+ r.raise_for_status()
+ with open(dest, 'wb') as f:
+ for chunk in r.iter_content(chunk_size=8192):
+ f.write(chunk)
+ print(f"Downloaded: {url} to {dest}")
+ except requests.exceptions.RequestException as e:
+ print(f"Error downloading {url}: {e}")
+ sys.exit(1)
+
+
+def main(args):
+
+ with open(args.json) as fh:
+ params = json.load(fh)
+ target_directory = params["output_data"][0]["extra_files_path"]
+
+ # Create output directory if none exists
+ if not os.path.exists(target_directory):
+ os.makedirs(target_directory)
+
+ # Check if the selected dataset exists
+ if args.name not in OMAMER_DATASETS:
+ print(f"Error: Selected dataset '{args.name}' not found.")
+ sys.exit(1)
+
+ # Download the selected OMAmer dataset
+ dataset = OMAMER_DATASETS[args.name]
+ url = OMAMER_DATASETS_URL.format(dataset=dataset)
+ base_name = os.path.splitext(dataset)[0]
+ destination_path = os.path.join(target_directory, dataset)
+ download_file(url, destination_path)
+
+ data_manager_entry = {
+ "value": dataset,
+ "name": base_name,
+ "version": args.version,
+ "path": dataset,
+ }
+
+ # Creates a JSON dictionary representing the Data Manager configuration
+ data_manager_json = {"data_tables": {"omamer": [data_manager_entry]}}
+
+ # Writes this JSON dictionary to the specified output file
+ with open(args.json, "w") as fh:
+ json.dump(data_manager_json, fh, indent=2, sort_keys=True)
+
+
+if __name__ == "__main__":
+ # Set up argparse to specify expected command line arguments
+ parser = argparse.ArgumentParser(description='Download data for OMAmer')
+ parser.add_argument('--name', default='Primates', choices=OMAMER_DATASETS.keys(), help='Select dataset to download')
+ parser.add_argument('--json', help='Path to JSON file')
+ parser.add_argument("--version", help="Omamer version")
+
+ args = parser.parse_args()
+
+ main(args)
diff -r 000000000000 -r d28438704310 data_manager/omamer.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/omamer.xml Wed Aug 14 15:42:38 2024 +0000
@@ -0,0 +1,45 @@
+
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+ macros.xml
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+
+ 10.1093/bioinformatics/btab219
+
+
diff -r 000000000000 -r d28438704310 data_manager_conf.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager_conf.xml Wed Aug 14 15:42:38 2024 +0000
@@ -0,0 +1,20 @@
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diff -r 000000000000 -r d28438704310 test-data/out.json
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/out.json Wed Aug 14 15:42:38 2024 +0000
@@ -0,0 +1,12 @@
+{
+ "data_tables": {
+ "omamer": [
+ {
+ "name": "Primates-v2.0.0",
+ "path": "Primates-v2.0.0.h5",
+ "value": "Primates-v2.0.0.h5",
+ "version": "2.0.2"
+ }
+ ]
+ }
+}
\ No newline at end of file
diff -r 000000000000 -r d28438704310 tool-data/omamer.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/omamer.loc.sample Wed Aug 14 15:42:38 2024 +0000
@@ -0,0 +1,8 @@
+# this is a tab separated file describing the location of OMAmer databases used for the
+# OMAmer annotation tool
+#
+# the columns are:
+# value name version path
+#
+# for example
+# Primates-v2.0.0 Primates 2.0.2 /tmp/database/omamer/database_omamer/Primates-v2.0.0
\ No newline at end of file
diff -r 000000000000 -r d28438704310 tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample Wed Aug 14 15:42:38 2024 +0000
@@ -0,0 +1,6 @@
+
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+ value, name, version, path
+
+
+