# HG changeset patch
# User dfornika
# Date 1558635397 14400
# Node ID 40ea0695a0a0b2341b17eda76e2b8945266b4bcf
# Parent  b60b0a9523db91816fc6c3a4f85801f639ea97a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 616f23916e8c71295e1456d6df585c351bd64f86-dirty

diff -r b60b0a9523db -r 40ea0695a0a0 data_manager/kraken2_build_database.py
--- a/data_manager/kraken2_build_database.py	Fri May 10 20:34:55 2019 -0400
+++ b/data_manager/kraken2_build_database.py	Thu May 23 14:16:37 2019 -0400
@@ -140,7 +140,6 @@
                 member.name = os.path.basename(member.name)
                 fh.extract(member, os.path.join(target_directory, database_path))
 
-
     data_table_entry = {
         'data_tables': {
             data_table_name: [
@@ -224,9 +223,12 @@
     args = [
         '--threads', str(kraken2_args["threads"]),
         '--download-taxonomy',
-        '--db', custom_database_name
+        '--db', custom_database_name,
     ]
 
+    if kraken2_args['skip_maps']:
+        args += '--skip-maps'
+
     subprocess.check_call(['kraken2-build'] + args, cwd=target_directory)
 
     args = [
@@ -283,6 +285,7 @@
     parser.add_argument('--special-database-type', dest='special_database_type', type=SpecialDatabaseTypes, choices=list(SpecialDatabaseTypes), help='type of special database to build (only applies to --database-type special)')
     parser.add_argument('--custom-fasta', dest='custom_fasta', help='fasta file for custom database (only applies to --database-type custom)')
     parser.add_argument('--custom-database-name', dest='custom_database_name', help='Name for custom database (only applies to --database-type custom)')
+    parser.add_argument('--skip-maps', dest='skip_maps', action='store_true', help='')
     args = parser.parse_args()
 
     data_manager_input = json.loads(open(args.data_manager_json).read())
@@ -330,6 +333,7 @@
     elif str(args.database_type) == 'custom':
         kraken2_args = {
             "custom_fasta": args.custom_fasta,
+            "skip_maps": args.skip_maps,
             "kmer_len": args.kmer_len,
             "minimizer_len": args.minimizer_len,
             "minimizer_spaces": args.minimizer_spaces,
diff -r b60b0a9523db -r 40ea0695a0a0 data_manager/kraken2_build_database.xml
--- a/data_manager/kraken2_build_database.xml	Fri May 10 20:34:55 2019 -0400
+++ b/data_manager/kraken2_build_database.xml	Thu May 23 14:16:37 2019 -0400
@@ -32,6 +32,7 @@
             --minimizer-spaces ${database_type.minimizer_spaces}
           #else if $database_type.database_type == "custom"
             --threads \${GALAXY_SLOTS:-1}
+            ${database_type.skip_maps}
             --custom-fasta ${database_type.custom_fasta}
             --custom-database-name ${database_type.custom_database_name}
             --kmer-len ${database_type.kmer_len}
@@ -68,6 +69,7 @@
             <when value="custom">
                 <param name="custom_fasta" type="data" format="fasta" multiple="False" optional="true" label="Select history item" />
                 <param name="custom_database_name" type="text" label="Name for this database" />
+                <param name="skip_maps" type="boolean" truevalue="--skip-maps" falsevalue="" label="Skip downloading accession number to taxid maps during taxonomy download." /> 
                 <expand macro="common_params" />
             </when>
             
diff -r b60b0a9523db -r 40ea0695a0a0 test-data/adapter.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/adapter.fa	Thu May 23 14:16:37 2019 -0400
@@ -0,0 +1,2 @@
+>sequence16|kraken:taxid|32630  Adapter sequence
+CAAGCAGAAGACGGCATACGAGATCTTCGAGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
diff -r b60b0a9523db -r 40ea0695a0a0 test-data/adapter.fastq
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/adapter.fastq	Thu May 23 14:16:37 2019 -0400
@@ -0,0 +1,4 @@
+@sequence16
+CAAGCAGAAGACGGCATACGAGATCTTCGAGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA
++
+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
diff -r b60b0a9523db -r 40ea0695a0a0 test-data/database/hash.k2d
Binary file test-data/database/hash.k2d has changed
diff -r b60b0a9523db -r 40ea0695a0a0 test-data/database/opts.k2d
Binary file test-data/database/opts.k2d has changed
diff -r b60b0a9523db -r 40ea0695a0a0 test-data/database/taxo.k2d
Binary file test-data/database/taxo.k2d has changed