# HG changeset patch
# User dfornika
# Date 1564185081 14400
# Node ID 5b355fcb1058419c6c6aa2deb0f4b07713b290e2
# Parent  bce135f3e3e8fb054c8dbb0684b9691265648c33
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 66c35bd1ec30e6cd16d16f3cc98c2c5b56533a48-dirty

diff -r bce135f3e3e8 -r 5b355fcb1058 data_manager/kraken2_build_database.py
--- a/data_manager/kraken2_build_database.py	Fri May 24 12:53:44 2019 -0400
+++ b/data_manager/kraken2_build_database.py	Fri Jul 26 19:51:21 2019 -0400
@@ -85,10 +85,12 @@
 
     args = [
         '--threads', str(kraken2_args["threads"]),
-        '--clean',
         '--db', database_path
     ]
 
+    if kraken2_args["clean"]:
+        args.append('--clean')
+
     subprocess.check_call(['kraken2-build'] + args, cwd=target_directory)
 
     data_table_entry = {
@@ -197,10 +199,12 @@
 
     args = [
         '--threads', str(kraken2_args["threads"]),
-        '--clean',
         '--db', database_path
     ]
 
+    if kraken2_args["clean"]:
+        args.append('--clean')
+
     subprocess.check_call(['kraken2-build'] + args, cwd=target_directory)
 
     data_table_entry = {
@@ -252,10 +256,12 @@
 
     args = [
         '--threads', str(kraken2_args["threads"]),
-        '--clean',
         '--db', custom_database_name
     ]
 
+    if kraken2_args["clean"]:
+        args.append('--clean')
+
     subprocess.check_call(['kraken2-build'] + args, cwd=target_directory)
 
     data_table_entry = {
@@ -286,6 +292,7 @@
     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='')
+    parser.add_argument('--clean', dest='clean', action='store_true', help='Clean up extra files')
     args = parser.parse_args()
 
     data_manager_input = json.loads(open(args.data_manager_json).read())
@@ -308,6 +315,7 @@
             "minimizer_len": args.minimizer_len,
             "minimizer_spaces": args.minimizer_spaces,
             "threads": args.threads,
+            "clean": args.clean,
         }
         data_manager_output = kraken2_build_standard(
             kraken2_args,
@@ -325,6 +333,7 @@
             "minimizer_len": args.minimizer_len,
             "minimizer_spaces": args.minimizer_spaces,
             "threads": args.threads,
+            "clean": args.clean,
         }
         data_manager_output = kraken2_build_special(
             kraken2_args,
@@ -338,6 +347,7 @@
             "minimizer_len": args.minimizer_len,
             "minimizer_spaces": args.minimizer_spaces,
             "threads": args.threads,
+            "clean": args.clean,
         }
         data_manager_output = kraken2_build_custom(
             kraken2_args,
diff -r bce135f3e3e8 -r 5b355fcb1058 data_manager/kraken2_build_database.xml
--- a/data_manager/kraken2_build_database.xml	Fri May 24 12:53:44 2019 -0400
+++ b/data_manager/kraken2_build_database.xml	Fri Jul 26 19:51:21 2019 -0400
@@ -5,6 +5,7 @@
             <param name="kmer_len" type="integer" value="35" label="K-mer length in BP" />
             <param name="minimizer_len" type="integer" value="31" label="Minimizer length" />
             <param name="minimizer_spaces" type="integer" value="6" label="Minimizer spaces" />
+            <param name="clean" type="boolean" truevalue="--clean" falsevalue="" label="Clean up extra files" />
         </xml>
     </macros>
     <description>database builder</description>
@@ -24,12 +25,14 @@
             --kmer-len ${database_type.kmer_len}
             --minimizer-len ${database_type.minimizer_len}
             --minimizer-spaces ${database_type.minimizer_spaces}
+            ${clean}
           #else if $database_type.database_type == "special"
             --threads \${GALAXY_SLOTS:-1}
             --special-database-type ${database_type.special_database_type}
             --kmer-len ${database_type.kmer_len}
             --minimizer-len ${database_type.minimizer_len}
             --minimizer-spaces ${database_type.minimizer_spaces}
+            ${clean}
           #else if $database_type.database_type == "custom"
             --threads \${GALAXY_SLOTS:-1}
             ${database_type.skip_maps}
@@ -38,6 +41,7 @@
             --kmer-len ${database_type.kmer_len}
             --minimizer-len ${database_type.minimizer_len}
             --minimizer-spaces ${database_type.minimizer_spaces}
+            ${clean}
           #end if
     ]]>
     </command>
@@ -54,7 +58,7 @@
             </when>
             <when value="minikraken">
                 <param name="minikraken2_version" type="select" multiple="false" label="Select MiniKraken2 database version to download">
-	                <option value="v2">Version 2</option>
+                    <option value="v2">Version 2</option>
                     <option value="v1">Version 1</option>
                 </param>
             </when>
@@ -72,7 +76,6 @@
                 <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>
-            
         </conditional>
     </inputs>
     <outputs>
@@ -84,6 +87,7 @@
             <param name="custom_fasta" value="adapter.fa" />
             <param name="custom_database_name" value="database" />
             <param name="skip_maps" value="true" />
+            <param name="clean" value="true" />
             <output name="out_file" value="kraken2_custom_data_manager.json" />
         </test>
     </tests>