# HG changeset patch
# User dfornika
# Date 1570077029 14400
# Node ID 5e00d9417f68f729f824698ddc7a118acff4c7dc
planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kma_index/ commit d9732cd3279d03dcc498bf2eb903f9e6120a9d85
diff -r 000000000000 -r 5e00d9417f68 data_manager/kma_build_index.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/kma_build_index.py Thu Oct 03 00:30:29 2019 -0400
@@ -0,0 +1,91 @@
+#!/usr/bin/env python
+
+from __future__ import print_function
+
+import argparse
+import errno
+import json
+import os
+import uuid
+import subprocess
+
+
+DATA_TABLE_NAME = "kma_index"
+
+def kma_build_index(kma_index_args, index_name, target_directory, data_table_name=DATA_TABLE_NAME):
+
+ args = [
+ '--k', str(kma_index_args["k"]),
+ '--k_t', str(kma_index_args["k_t"]),
+ '--k_i', str(kma_index_args["k_i"]),
+ '--ML', str(kma_index_args["ML"]),
+ '--ht', str(kma_index_args["ht"]),
+ '--hq', str(kma_index_args["hq"]),
+ str(kma_index_args["fasta"]),
+ ]
+
+ subprocess.check_call(['kma index'] + args, cwd=target_directory)
+
+ data_table_entry = {
+ 'data_tables': {
+ data_table_name: [
+ {
+ "value": uuid.uuid4(),
+ "name": index_name,
+ "path": "seq",
+ }
+ ]
+ }
+ }
+
+ return data_table_entry
+
+
+def main(args):
+
+ data_manager_input = json.loads(open(args.data_manager_json).read())
+
+ target_directory = data_manager_input['output_data'][0]['extra_files_path']
+
+ try:
+ os.mkdir( target_directory )
+ except OSError as exc:
+ if exc.errno == errno.EEXIST and os.path.isdir( target_directory ):
+ pass
+ else:
+ raise
+
+ data_manager_output = {}
+
+ kma_index_args = {
+ "k": args.k,
+ "k_t": args.k_t,
+ "k_i": args.k_i,
+ "ML": args.ML,
+ "ht": args.ht,
+ "hq": args.hq,
+ "fasta": args.fasta,
+ }
+
+ data_manager_output = kma_build_index(
+ kma_index_args,
+ args.index_name,
+ target_directory,
+ )
+
+ open(args.data_manager_json, 'w').write(json.dumps(data_manager_output))
+
+
+if __name__ == "__main__":
+ parser = argparse.ArgumentParser()
+ parser.add_argument('data_manager_json')
+ parser.add_argument('--k', dest='k', type=int, default=16, help='')
+ parser.add_argument('--k_t', dest='k_t', type=int, default=16, help='')
+ parser.add_argument('--k_i', dest='k_i', type=int, default=16, help='')
+ parser.add_argument('--ML', dest='ML', type=int, default=16, help='')
+ parser.add_argument('--ht', dest='ht', type=float, default=1.0, help='')
+ parser.add_argument('--hq', dest='hq', type=float, default=1.0, help='')
+ parser.add_argument('--name', dest='index_name',help='')
+ parser.add_argument('fasta', nargs='+', help='fasta file(s) to index')
+ args = parser.parse_args()
+ main(args)
diff -r 000000000000 -r 5e00d9417f68 data_manager/kma_build_index.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/kma_build_index.xml Thu Oct 03 00:30:29 2019 -0400
@@ -0,0 +1,49 @@
+
+
+ kma index builder
+
+ kma
+
+ kma -v
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ @article{clausen2018rapid,
+ title={Rapid and precise alignment of raw reads against redundant databases with KMA},
+ author={Clausen, Philip TLC and Aarestrup, Frank M and Lund, Ole},
+ journal={BMC bioinformatics},
+ volume={19},
+ number={1},
+ pages={307},
+ year={2018},
+ publisher={BioMed Central}
+ }
+
+
+
diff -r 000000000000 -r 5e00d9417f68 data_manager_conf.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager_conf.xml Thu Oct 03 00:30:29 2019 -0400
@@ -0,0 +1,18 @@
+
+
+
+
+
+
+
diff -r 000000000000 -r 5e00d9417f68 tool-data/kma_index.loc.sample
diff -r 000000000000 -r 5e00d9417f68 tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample Thu Oct 03 00:30:29 2019 -0400
@@ -0,0 +1,8 @@
+
+
+
+
+