# HG changeset patch
# User iuc
# Date 1642014439 0
# Node ID b5bca6d58e4c69f301e957a674b8273f80e99116
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_genomic_super_signature_ravmodels commit 1aadd5dce3b254e7714c2fdd39413029fd4b9b7a"
diff -r 000000000000 -r b5bca6d58e4c README
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/README Wed Jan 12 19:07:19 2022 +0000
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+Adds new entries to data tables for GenomicSuperSignature Replicable Axes of Variation (RAV) models (RAVmodels). See also https://www.biorxiv.org/content/10.1101/2021.05.26.445900v1.
\ No newline at end of file
diff -r 000000000000 -r b5bca6d58e4c data_manager/data_manager_genomic_super_signature_ravmodels.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/data_manager_genomic_super_signature_ravmodels.py Wed Jan 12 19:07:19 2022 +0000
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+#!/usr/bin/env python
+# Dan Blankenberg
+
+
+import argparse
+import json
+import os
+import re
+import shutil
+import urllib.request
+
+
+OUTPUT_BASE_NAME = 'RAVmodel.rds'
+
+BUCKET_NAME = "genomic_super_signature"
+RAVMODEL_NAME = "RAVmodel_{prior}.rds"
+PRIOR_URL = "https://storage.googleapis.com/{bucket_name}/{prior_filename}"
+
+
+def get_prior_url(prior):
+ return PRIOR_URL.format(bucket_name=BUCKET_NAME, prior_filename=RAVMODEL_NAME.format(prior=prior))
+
+
+def clean(text):
+ return re.sub(r'[^\w\-_\.]', '-', text)
+
+
+def main():
+ parser = argparse.ArgumentParser()
+ parser.add_argument('--output', dest='output', action='store', type=str, default=None)
+ parser.add_argument('--json', dest='json', action='store', type=str, default=None)
+ parser.add_argument('--dbkey', dest='dbkey', action='store', type=str, default=None, help='dbkey')
+ parser.add_argument('--name', dest='name', action='store', type=str, default=None)
+ parser.add_argument('--id', dest='id', action='store', type=str, default=None)
+ parser.add_argument('--prior', dest='prior', action='store', type=str, default=None)
+ parser.add_argument('--url', dest='url', action='store', type=str, default=None)
+ parser.add_argument('--input', dest='input', action='store', type=str, default=None)
+ parser.add_argument('--symlink', dest='symlink', action='store_true', default=False)
+ parser.add_argument('--version', dest='version', action='store', type=str, default="0")
+ parser.add_argument('--tablename', dest='tablename', action='store', type=str, default="genomic_super_signature_ravmodels")
+ args = parser.parse_args()
+
+ os.makedirs(args.output, exist_ok=True)
+ output_filename = os.path.join(args.output, OUTPUT_BASE_NAME)
+ if args.symlink:
+ assert args.input, "You must provide a filename when using symlink functionality."
+ os.symlink(args.input, output_filename)
+ else:
+ url = args.url
+ if args.prior:
+ url = get_prior_url(args.prior)
+ if url:
+ urllib.request.urlretrieve(url, output_filename)
+ else:
+ assert args.input, "You must provide a filename, prior, or URL."
+ shutil.copyfile(args.input, output_filename)
+ data_manager_dict = {'data_tables': {args.tablename: [dict(value=clean(args.id), dbkey=args.dbkey, version=args.version, name=args.name, path=OUTPUT_BASE_NAME)]}}
+
+ with open(args.json, 'w') as fh:
+ json.dump(data_manager_dict, fh, sort_keys=True)
+
+
+if __name__ == "__main__":
+ main()
diff -r 000000000000 -r b5bca6d58e4c data_manager/data_manager_genomic_super_signature_ravmodels.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/data_manager_genomic_super_signature_ravmodels.xml Wed Jan 12 19:07:19 2022 +0000
@@ -0,0 +1,89 @@
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+ into built-in cache
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+ python
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+**What it does**
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+Fetches a reference RAVmodel from various sources (Google Cloud, URL, Galaxy History, or a server file) and populates the "genomic_super_signature_ravmodels" data table.
+
+------
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+.. class:: infomark
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+**Notice:** If you leave name or id blank, it will be generated automatically.
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diff -r 000000000000 -r b5bca6d58e4c data_manager_conf.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager_conf.xml Wed Jan 12 19:07:19 2022 +0000
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diff -r 000000000000 -r b5bca6d58e4c test-data/RAVmodel_prior_C2.data_manager_json
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/RAVmodel_prior_C2.data_manager_json Wed Jan 12 19:07:19 2022 +0000
@@ -0,0 +1,1 @@
+{"data_tables": {"genomic_super_signature_ravmodels": [{"dbkey": "hg38", "name": "MSigDB C2 (curated gene sets)", "path": "RAVmodel.rds", "value": "C2", "version": "0"}]}}
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diff -r 000000000000 -r b5bca6d58e4c tool-data/genomic_super_signature_ravmodels.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/genomic_super_signature_ravmodels.loc.sample Wed Jan 12 19:07:19 2022 +0000
@@ -0,0 +1,1 @@
+#
diff -r 000000000000 -r b5bca6d58e4c tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample Wed Jan 12 19:07:19 2022 +0000
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+ value, dbkey, version, name, path
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