Mercurial > repos > iuc > data_manager_build_kraken2_database

changeset 4:0eebe086fd58 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit fed92935f1f0b52173d2fddbdd2bbf44e802b51e"
author iuc
date Mon, 23 Nov 2020 20:49:52 +0000
parents 19b6a2f0dbe2
children 2f27f3b86827
files data_manager/kraken2_build_database.py data_manager/kraken2_build_database.xml
diffstat 2 files changed, 18 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- a/data_manager/kraken2_build_database.py	Sun Nov 22 12:45:56 2020 +0000
+++ b/data_manager/kraken2_build_database.py	Mon Nov 23 20:49:52 2020 +0000
@@ -59,6 +59,7 @@
         "kmer-len", str(kraken2_args["kmer_len"]),
         "minimizer-len", str(kraken2_args["minimizer_len"]),
         "minimizer-spaces", str(kraken2_args["minimizer_spaces"]),
+        "load-factor", str(kraken2_args["load_factor"]),
     ])
 
     database_name = " ".join([
@@ -68,6 +69,7 @@
         "kmer-len=" + str(kraken2_args["kmer_len"]) + ",",
         "minimizer-len=" + str(kraken2_args["minimizer_len"]) + ",",
         "minimizer-spaces=" + str(kraken2_args["minimizer_spaces"]) + ")",
+        "load-factor", str(kraken2_args["load_factor"]),
     ])
 
     database_path = database_value
@@ -78,6 +80,7 @@
         '--kmer-len', str(kraken2_args["kmer_len"]),
         '--minimizer-len', str(kraken2_args["minimizer_len"]),
         '--minimizer-spaces', str(kraken2_args["minimizer_spaces"]),
+        '--load-factor', str(kraken2_args["load_factor"]),
         '--db', database_path
     ]
 
@@ -172,6 +175,7 @@
         "kmer-len", str(kraken2_args["kmer_len"]),
         "minimizer-len", str(kraken2_args["minimizer_len"]),
         "minimizer-spaces", str(kraken2_args["minimizer_spaces"]),
+        "load-factor", str(kraken2_args["load_factor"]),
     ])
 
     database_name = " ".join([
@@ -181,6 +185,7 @@
         "kmer-len=" + str(kraken2_args["kmer_len"]) + ",",
         "minimizer-len=" + str(kraken2_args["minimizer_len"]) + ",",
         "minimizer-spaces=" + str(kraken2_args["minimizer_spaces"]) + ")",
+        "load-factor=" + str(kraken2_args["load_factor"]) + ")",
     ])
 
     database_path = database_value
@@ -191,6 +196,7 @@
         '--kmer-len', str(kraken2_args["kmer_len"]),
         '--minimizer-len', str(kraken2_args["minimizer_len"]),
         '--minimizer-spaces', str(kraken2_args["minimizer_spaces"]),
+        '--load-factor', str(kraken2_args["load_factor"]),
         '--db', database_path
     ]
 
@@ -247,6 +253,7 @@
         '--kmer-len', str(kraken2_args["kmer_len"]),
         '--minimizer-len', str(kraken2_args["minimizer_len"]),
         '--minimizer-spaces', str(kraken2_args["minimizer_spaces"]),
+        '--load-factor', str(kraken2_args["load_factor"]),
         '--db', custom_database_name
     ]
 
@@ -282,6 +289,7 @@
     parser.add_argument('--kmer-len', dest='kmer_len', type=int, default=35, help='kmer length')
     parser.add_argument('--minimizer-len', dest='minimizer_len', type=int, default=31, help='minimizer length')
     parser.add_argument('--minimizer-spaces', dest='minimizer_spaces', default=6, help='minimizer spaces')
+    parser.add_argument('--load-factor', dest='load_factor', type=float, default=0.7, help='load factor')
     parser.add_argument('--threads', dest='threads', default=1, help='threads')
     parser.add_argument('--database-type', dest='database_type', type=KrakenDatabaseTypes, choices=list(KrakenDatabaseTypes), required=True, help='type of kraken database to build')
     parser.add_argument('--minikraken2-version', dest='minikraken2_version', type=Minikraken2Versions, choices=list(Minikraken2Versions), help='MiniKraken2 version (only applies to --database-type minikraken)')
@@ -312,6 +320,7 @@
             "kmer_len": args.kmer_len,
             "minimizer_len": args.minimizer_len,
             "minimizer_spaces": args.minimizer_spaces,
+            "load_factor": args.load_factor,
             "threads": args.threads,
             "clean": args.clean,
         }
@@ -330,6 +339,7 @@
             "kmer_len": args.kmer_len,
             "minimizer_len": args.minimizer_len,
             "minimizer_spaces": args.minimizer_spaces,
+            "load_factor": args.load_factor,
             "threads": args.threads,
             "clean": args.clean,
         }
@@ -344,6 +354,7 @@
             "kmer_len": args.kmer_len,
             "minimizer_len": args.minimizer_len,
             "minimizer_spaces": args.minimizer_spaces,
+            "load_factor": args.load_factor,
             "threads": args.threads,
             "clean": args.clean,
         }
--- a/data_manager/kraken2_build_database.xml	Sun Nov 22 12:45:56 2020 +0000
+++ b/data_manager/kraken2_build_database.xml	Mon Nov 23 20:49:52 2020 +0000
@@ -1,16 +1,18 @@
 <?xml version="1.0"?>
-<tool id="kraken2_build_database" name="Kraken2" tool_type="manage_data" version="2.0.8_beta+galaxy2" profile="18.09">
+<tool id="kraken2_build_database" name="Kraken2" tool_type="manage_data" version="@TOOL_VERSION@" profile="18.09">
     <macros>
+        <token name="@TOOL_VERSION@">2.1.1</token>
         <xml name="common_params">
             <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="load_factor" type="float" value="0.7" min="0" max="1" label="Load factor" help="Proportion of the hash table to be populated" />
             <param name="clean" type="boolean" truevalue="--clean" falsevalue="" checked="true" label="Clean up extra files" />
         </xml>
     </macros>
     <description>database builder</description>
     <requirements>
-        <requirement type="package" version="2.0.8_beta">kraken2</requirement>
+        <requirement type="package" version="@TOOL_VERSION@">kraken2</requirement>
         <requirement type="package" version="3.7">python</requirement>
     </requirements>
     <version_command>kraken2 -version | head -n 1 | awk '{print $NF}'</version_command>
@@ -26,6 +28,7 @@
             --kmer-len ${database_type.kmer_len}
             --minimizer-len ${database_type.minimizer_len}
             --minimizer-spaces ${database_type.minimizer_spaces}
+            --load-factor ${database_type.load_factor}
             ${database_type.clean}
           #else if $database_type.database_type == "special"
             --threads \${GALAXY_SLOTS:-1}
@@ -33,6 +36,7 @@
             --kmer-len ${database_type.kmer_len}
             --minimizer-len ${database_type.minimizer_len}
             --minimizer-spaces ${database_type.minimizer_spaces}
+            --load-factor ${database_type.load_factor}
             ${database_type.clean}
           #else if $database_type.database_type == "custom"
             --threads \${GALAXY_SLOTS:-1}
@@ -42,6 +46,7 @@
             --kmer-len ${database_type.kmer_len}
             --minimizer-len ${database_type.minimizer_len}
             --minimizer-spaces ${database_type.minimizer_spaces}
+            --load-factor ${database_type.load_factor}
             ${database_type.clean}
           #end if
     ]]>