# HG changeset patch
# User iuc
# Date 1629960885 0
# Node ID ef7f9e2f32f21178b9364ec879524cf305acd68f
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
diff -r 000000000000 -r ef7f9e2f32f2 data_manager/funannotate.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/funannotate.py Thu Aug 26 06:54:45 2021 +0000
@@ -0,0 +1,58 @@
+#!/usr/bin/env python
+
+import argparse
+import json
+import operator
+import os
+import subprocess
+import sys
+from datetime import datetime
+
+
+if __name__ == "__main__":
+
+ parser = argparse.ArgumentParser()
+ parser.add_argument('--partial', dest='partial', action='store_true', help='Only download a small subset of data (for testing)')
+ parser.add_argument("version_id")
+ parser.add_argument("datatable_name")
+ parser.add_argument("galaxy_datamanager_filename")
+ args = parser.parse_args()
+
+ with open(args.galaxy_datamanager_filename) as fh:
+ config = json.load(fh)
+
+ output_directory = config.get("output_data", [{}])[0].get("extra_files_path", None)
+ data_manager_dict = {}
+ data_manager_dict["data_tables"] = config.get("data_tables", {})
+ data_manager_dict["data_tables"][args.datatable_name] = data_manager_dict[
+ "data_tables"
+ ].get(args.datatable_name, [])
+
+ os.mkdir(output_directory)
+ cmd_args = ['funannotate', 'setup', '-d', output_directory, '-b', 'all']
+ if args.partial:
+ cmd_args += ['-i', 'merops', '-b', 'eukaryota']
+ proc = subprocess.Popen(args=cmd_args, shell=False, cwd=output_directory)
+ return_code = proc.wait()
+ if return_code:
+ print("Error downloading Funannotate database.", file=sys.stderr)
+ sys.exit(return_code)
+
+ version_id = datetime.today().strftime('%Y-%m-%d-%H%M%S')
+
+ version = '1.0'
+
+ data_manager_dict["data_tables"][args.datatable_name].append(
+ dict(
+ value=version_id,
+ description="Funannotate database %s" % version_id,
+ format_version=version,
+ path=output_directory,
+ )
+ )
+
+ data_manager_dict["data_tables"][args.datatable_name].sort(
+ key=operator.itemgetter("value"), reverse=True
+ )
+ with open(args.galaxy_datamanager_filename, "w") as fh:
+ json.dump(data_manager_dict, fh, indent=2, sort_keys=True)
diff -r 000000000000 -r ef7f9e2f32f2 data_manager/funannotate.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/funannotate.xml Thu Aug 26 06:54:45 2021 +0000
@@ -0,0 +1,39 @@
+
+
+ funannotate
+
+ funannotate check --show-versions
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ 10.5281/zenodo.4054262
+
+
diff -r 000000000000 -r ef7f9e2f32f2 data_manager_conf.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager_conf.xml Thu Aug 26 06:54:45 2021 +0000
@@ -0,0 +1,19 @@
+
+
+
+
+
+
+
+
diff -r 000000000000 -r ef7f9e2f32f2 test-data/funannotate.loc
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/funannotate.loc Thu Aug 26 06:54:45 2021 +0000
@@ -0,0 +1,9 @@
+# this is a tab separated file describing the location of funannotate databases used for the
+# funannotate annotation tool
+#
+# the columns are:
+# value description format_version path
+#
+# for example
+# 2021-07-20-120000 Funannotate database 2021-07-20-120000 1.0 /tmp/database/funannotate/2021-07-20-120000
+# 2021-05-27-120000 Funannotate database 2021-05-27-120000 3.0 /tmp/database/funannotate/2021-05-27-120000
diff -r 000000000000 -r ef7f9e2f32f2 tool-data/funannotate.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/funannotate.loc.sample Thu Aug 26 06:54:45 2021 +0000
@@ -0,0 +1,8 @@
+# this is a tab separated file describing the location of funannotate databases used for the
+# funannotate annotation tool
+#
+# the columns are:
+# value description format_version path
+#
+# for example
+# 2021-07-20-120000 Funannotate database 2021-07-20-120000 1.0 /tmp/database/funannotate/funannotate/2021-07-20-120000
diff -r 000000000000 -r ef7f9e2f32f2 tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample Thu Aug 26 06:54:45 2021 +0000
@@ -0,0 +1,6 @@
+
+
+ value, description, format_version, path
+
+
+
diff -r 000000000000 -r ef7f9e2f32f2 tool_data_table_conf.xml.test
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.test Thu Aug 26 06:54:45 2021 +0000
@@ -0,0 +1,6 @@
+
+
+ value, description, format_version, path
+
+
+