# HG changeset patch
# User iuc
# Date 1585345823 14400
# Node ID 26a6f95e82c8d31508438dcaa58d881285fbe0a8
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
diff -r 000000000000 -r 26a6f95e82c8 data_manager/data_manager.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/data_manager.py Fri Mar 27 17:50:23 2020 -0400
@@ -0,0 +1,91 @@
+import argparse
+import json
+import os
+import shutil
+import tarfile
+try:
+ # For Python 3.0 and later
+ from urllib.request import Request, urlopen
+except ImportError:
+ # Fall back to Python 2 imports
+ from urllib2 import Request, urlopen
+
+ZENODO = {
+ "mitos": "2683856",
+ "mitos2": "3685310"
+}
+NAMES = {
+ "mitos1-refdata": "RefSeq39 + MiTFi tRNA models",
+ "refseq39": "RefSeq39 (equivalent to MITOS1 data)",
+ "refseq63m": "RefSeq63 Metazoa",
+ "refseq63f": "RefSeq63 Fungi",
+ "refseq63o": "RefSeq63 Opisthokonta",
+ "refseq89m": "RefSeq89 Metazoa",
+ "refseq89f": "RefSeq89 Fungi",
+ "refseq89o": "RefSeq89 Opisthokonta"
+}
+
+
+def url_download(tpe, db, workdir):
+ """
+ download http://ab.inf.uni-tuebingen.de/data/software/megan6/download/FNAME
+ to workdir
+ and unzip
+
+ return the name of the resulting dir
+ """
+ tarfname = os.path.join(workdir, db + ".tar.bz")
+ if not os.path.exists(workdir):
+ os.makedirs(workdir)
+ src = None
+ dst = None
+ try:
+ req = Request("https://zenodo.org/record/{zenodoid}/files/{db}.tar.bz2?download=1".format(zenodoid=ZENODO[tpe], db=db))
+ src = urlopen(req)
+ with open(tarfname, 'wb') as dst:
+ while True:
+ chunk = src.read(2**10)
+ if chunk:
+ dst.write(chunk)
+ else:
+ break
+ finally:
+ if src:
+ src.close()
+ with tarfile.open(tarfname, "r:bz2") as tar:
+ dirname = tar.getnames()[0]
+ tar.extractall(workdir)
+ os.remove(tarfname)
+ return dirname
+
+
+def main(tpe, db, outjson):
+ workdir = os.getcwd()
+
+ path = url_download(tpe, db, workdir)
+
+ data_manager_entry = {}
+ data_manager_entry['value'] = db
+ data_manager_entry['name'] = NAMES[db]
+ data_manager_entry['type'] = tpe
+ data_manager_entry['path'] = path
+ data_manager_json = dict(data_tables=dict(mitos=data_manager_entry))
+
+ with open(outjson) as f:
+ params = json.loads(f.read())
+ target_directory = params['output_data'][0]['extra_files_path']
+ os.mkdir(target_directory)
+ # output_path = os.path.abspath(os.path.join(os.getcwd(), 'mitos'))
+ shutil.move(os.path.join(workdir, path), target_directory)
+ with open(outjson, 'w') as fh:
+ fh.write(json.dumps(data_manager_json, sort_keys=True))
+
+
+if __name__ == '__main__':
+ parser = argparse.ArgumentParser(description='Create data manager json.')
+ parser.add_argument('--out', action='store', help='JSON filename')
+ parser.add_argument('--type', action='store', help='mitos version')
+ parser.add_argument('--db', action='store', help='db name')
+ args = parser.parse_args()
+
+ main(args.type, args.db, args.out)
diff -r 000000000000 -r 26a6f95e82c8 data_manager/data_manager_mitos.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/data_manager_mitos.xml Fri Mar 27 17:50:23 2020 -0400
@@ -0,0 +1,86 @@
+
+
+ reference data downloader
+
+ python
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+
+This data manager downloads MITOS and MITOS2 reference data for use in Galaxy.
+
+For MITOS the reference data includes
+
+- protein data bases derived from RefSeq release 39 (see Bernt et al. 2012)
+- covariance models for tRNAs and rRNAs as described in Jühling et al 2012
+
+Data is downloaded from https://zenodo.org/record/2683856.
+
+For MITOS2 the reference data sets are available for three different taxons
+
+- Metazoa
+- Fungi
+- Opisthokonta
+
+these have been computed for RefSeq release 63 and 89. In addition the reference data
+for MITOS1 has been converted to be usable in MITOS2.
+contains
+
+The reference data sets contain:
+
+- protein data bases derived from the corresponding RefSeq release Donath et al. 2019
+- covariance models computed for the data in the RefSeq releas based on the MITOS1 models
+- in addition for Metazoa Release 63 also hidden markov models are available as described in Al Arab et al. 2017
+
+Data is downloaded from https://zenodo.org/record/3685310.
+
+
+ 10.1016/j.ympev.2012.08.023
+ 10.1093/nar/gkr1131
+ 10.1016/j.ympev.2016.09.024
+ 10.1093/nar/gkz833
+
+
+
diff -r 000000000000 -r 26a6f95e82c8 data_manager_conf.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager_conf.xml Fri Mar 27 17:50:23 2020 -0400
@@ -0,0 +1,20 @@
+
+
+
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+
diff -r 000000000000 -r 26a6f95e82c8 test-data/mitos.loc
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mitos.loc Fri Mar 27 17:50:23 2020 -0400
@@ -0,0 +1,4 @@
+mitos1-refdata RefSeq39 + MiTFi tRNA models mitos /tmp/tmpbtwefN/tmpiplugx/tmpydhEfm/database/data_manager_tool-datacoy8bz/mitos/mitos1-refdata
+mitos1-refdata RefSeq39 + MiTFi tRNA models mitos /tmp/tmpGIPfAb/tmpfKzrSO/tmpOaxm5C/database/data_manager_tool-data6ViNKD/mitos/mitos1-refdata
+mitos1-refdata RefSeq39 + MiTFi tRNA models mitos /tmp/tmpoaKkwC/tmprSa8eg/tmpT61Fpn/database/data_manager_tool-data0wohya/mitos/mitos1-refdata
+mitos1-refdata RefSeq39 + MiTFi tRNA models mitos /tmp/tmpo_lErk/tmpzfa6qz/tmpCY3yzt/database/data_manager_tool-dataCMEecR/mitos/mitos1-refdata
diff -r 000000000000 -r 26a6f95e82c8 test-data/mitos_refseq39.json
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mitos_refseq39.json Fri Mar 27 17:50:23 2020 -0400
@@ -0,0 +1,1 @@
+{"data_tables": {"mitos": {"name": "RefSeq39 + MiTFi tRNA models", "path": "mitos1-refdata", "type": "mitos", "value": "mitos1-refdata"}}}
\ No newline at end of file
diff -r 000000000000 -r 26a6f95e82c8 tool-data/mitos.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/mitos.loc.sample Fri Mar 27 17:50:23 2020 -0400
@@ -0,0 +1,8 @@
+# consists of 4 tab separated columns:
+# - value identifier
+# - name the name shown in the tool form
+# - type mitos/mitos2
+# - path the directory containing the reference data
+#
+# example:
+# mitos1-refdata RefSeq39 + MiTFi tRNA models mitos /tmp/tmpSp4v2Y/tmpR7DRNf/tmp53wbgs/database/data_manager_tool-dataWhw0Ns/mitos/mitos1-refdata
diff -r 000000000000 -r 26a6f95e82c8 tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample Fri Mar 27 17:50:23 2020 -0400
@@ -0,0 +1,8 @@
+
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+ value, name, type, path
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diff -r 000000000000 -r 26a6f95e82c8 tool_data_table_conf.xml.test
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.test Fri Mar 27 17:50:23 2020 -0400
@@ -0,0 +1,7 @@
+
+
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+ value, name, type, path
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+