# HG changeset patch
# User rplanel
# Date 1694509605 0
# Node ID a04c5659aac33c7af0f2e70cb1f327cb5910c815
planemo upload for repository https://gitlab.pasteur.fr/galaxy-team/galaxy-tools/-/tree/master/data_managers/data_manager_defense_finder commit cd90d22094f1128738ca4614b51d81af00a83d50
diff -r 000000000000 -r a04c5659aac3 data_manager/data_manager_defense_finder.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/data_manager_defense_finder.xml Tue Sep 12 09:06:45 2023 +0000
@@ -0,0 +1,32 @@
+
+ genotype data fetcher
+
+ 1.1.1
+
+
+ defense-finder
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ 10.1038/s41467-022-30269-9
+ 10.24072/pcjournal.250
+
+
diff -r 000000000000 -r a04c5659aac3 data_manager/defense_finder_models_fetcher.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/defense_finder_models_fetcher.py Tue Sep 12 09:06:45 2023 +0000
@@ -0,0 +1,60 @@
+#!/usr/bin/env python
+
+import argparse
+import json
+
+import subprocess
+import sys
+from pathlib import Path
+
+
+def main(args):
+ dataset_basename = "defense-finder-models"
+ models_version = args.version
+ output_file = args.output
+ dataset_value = f"{dataset_basename}_{models_version}"
+ with open(output_file) as fh:
+ params = json.load(fh)
+ target_directory = Path(params["output_data"][0]["extra_files_path"])
+ target_directory.mkdir(parents=True, exist_ok=True)
+ # download models with macsydata
+ args = [
+ "defense-finder",
+ "update",
+ "--models-dir",
+ dataset_value,
+ ]
+
+ proc = subprocess.Popen(args=args, shell=False, cwd=target_directory)
+ return_code = proc.wait()
+ if return_code:
+ print("Error building index.", file=sys.stderr)
+ sys.exit(return_code)
+
+ data_table_entry = dict(
+ value=dataset_value,
+ dbkey=dataset_basename,
+ version=models_version,
+ name=f"Defense Finder models (version {models_version})",
+ description="MacSyFinder models allowing for a systematic search of anti-phage systems",
+ path=dataset_value,
+ )
+
+ data_manager_json = dict(data_tables={"defense-finder": data_table_entry})
+
+ # move dir to final target dir
+ # shutil.move(workdir / dataset_name, target_directory_tax)
+ # data_manager_json = dict(data_tables=dict(pasteurqtl=data_table_entry))
+ with open(output_file, "w") as fh:
+ json.dump(data_manager_json, fh, sort_keys=True)
+
+
+if __name__ == "__main__":
+ parser = argparse.ArgumentParser(description="Create data manager json.")
+ parser.add_argument("--out", dest="output", action="store", help="JSON filename")
+ parser.add_argument(
+ "--version", dest="version", action="store", default="1", help="dataset version"
+ )
+
+ args = parser.parse_args()
+ main(args)
diff -r 000000000000 -r a04c5659aac3 data_manager_conf.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager_conf.xml Tue Sep 12 09:06:45 2023 +0000
@@ -0,0 +1,23 @@
+
+
+
+
+
+
+
+
\ No newline at end of file
diff -r 000000000000 -r a04c5659aac3 test-data/defense_finder_test_data_manager.json
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/defense_finder_test_data_manager.json Tue Sep 12 09:06:45 2023 +0000
@@ -0,0 +1,1 @@
+{"data_tables": {"defense-finder": {"dbkey": "defense-finder-models", "description": "MacSyFinder models allowing for a systematic search of anti-phage systems", "name": "Defense Finder models (version 1.2.2)", "path": "defense-finder-models_1.2.2", "value": "defense-finder-models_1.2.2", "version": "1.2.2"}}}
\ No newline at end of file
diff -r 000000000000 -r a04c5659aac3 tool-data/defense-finder.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/defense-finder.loc.sample Tue Sep 12 09:06:45 2023 +0000
@@ -0,0 +1,7 @@
+# this is a tab separated file describing the location of defense finder models
+#
+# the columns are:
+# value, dbkey, name, version, description, path
+#
+# for example
+# defense-finder-models_1.2.2 defense-finder-models Defense Finder models (version 1.2.2) 1.2.2 MacSyFinder models allowing for a systematic search of anti-phage systems /depot/data/galaxy/defense-finder/defense-finder-models_1.2.2
diff -r 000000000000 -r a04c5659aac3 tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample Tue Sep 12 09:06:45 2023 +0000
@@ -0,0 +1,6 @@
+
+
+ value, dbkey, name, version, description, path
+
+
+
\ No newline at end of file
diff -r 000000000000 -r a04c5659aac3 tool_data_table_conf.xml.test
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.test Tue Sep 12 09:06:45 2023 +0000
@@ -0,0 +1,6 @@
+
+
+ value, dbkey, name, version, description, path
+
+
+
\ No newline at end of file